diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..3189fd0
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,3 @@
+eFORGE was developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network.
+
+The code, webserver and database are currently maintained by Charles Breeze and Javier Herrero.
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..94a0453
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,621 @@
+ GNU GENERAL PUBLIC LICENSE
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+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
diff --git a/database/README.txt b/database/README.txt
new file mode 100755
index 0000000..e583945
--- /dev/null
+++ b/database/README.txt
@@ -0,0 +1,40 @@
+This directory contains the scripts and files necessary to rebuild the eFORGE database from scratch.
+
+In summary, the steps are:
+- Create an empty DB
+- Load the information about the arrays
+- Load the dataset with DHS, Histone peaks, etc
+- Move the DB to its final destination
+
+1. CREATE AN EMPTY DATABASE
+
+Please refer to the help of init_db.pl for information about the different options
+
+rm eforge_1.2.db
+perl init_db.pl --db_name eforge_1.2.db
+
+2. LOAD THE ARRAYS
+
+Please refer to the help of load_450k_array.pl for information about the different options
+
+perl load_450k_array.pl --work_dir input --db_name eforge_1.2.db
+perl load_27k_array.pl --work_dir input --db_name eforge_1.2.db
+
+3. LOAD THE DATASETS
+
+Please refer to the help of load_dataset.pl for information about the different options
+
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/
+perl load_dataset.pl --db_name eforge_1.2.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/
+perl load_dataset.pl --db_name eforge_1.2.db --tag blueprint --name 'Blueprint - DHS' --decode_file blueprint.decode --work_dir input/blueprint/
+
+4. MOVE THE DATABASE TO ITS FINAL LOCATION
+
+mv eforge_1.2.db ..
diff --git a/database/blueprint.decode b/database/blueprint.decode
new file mode 100644
index 0000000..eb41245
--- /dev/null
+++ b/database/blueprint.decode
@@ -0,0 +1,31 @@
+file lab datatype cell tissue shortcell individual acc url
+BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS/BP_DG-75_d01.DNase.hotspot_v3.20130819.bed.gz
+S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00C0J41.DNase.hotspot_v3.20141014.bed.gz
+BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS/BP_U-266_d01.DNase.hotspot_v3.20130819.bed.gz
+S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00CR241.DNase.hotspot_v3.20141014.bed.gz
+BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS/BP_Z-138_d01.DNase.hotspot_v3.20130819.bed.gz
+S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00CS041.DNase.hotspot_v3.20141014.bed.gz
+C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0010K46.DNase.hotspot_v3.20130415.bed.gz
+S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00CTZ41.DNase.hotspot_v3.20141014.bed.gz
+C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0011I43.DNase.hotspot_v3.20130415.bed.gz
+S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00EPZ41.DNase.hotspot_v3.20141014.bed.gz
+C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C001UY46.DNase.hotspot_v3.20130415.bed.gz
+S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00HRJ41.DNase.hotspot_v3.20141014.bed.gz
+C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C004084E.DNase.hotspot_v3.20130415.bed.gz
+S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00HSH41.DNase.hotspot_v3.20141014.bed.gz
+C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C005PS4E.DNase.hotspot_v3.20130819.bed.gz
+S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00HTF41.DNase.hotspot_v3.20141014.bed.gz
+C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS/C005VG45.DNase.hotspot_v3.20130819.bed.gz
+S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00JPF41.DNase.hotspot_v3.20141014.bed.gz
+C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS/C006NS47.DNase.hotspot_v3.20130819.bed.gz
+S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00JQD41.DNase.hotspot_v3.20141014.bed.gz
+C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS/C006UE47.DNase.hotspot_v3.20130819.bed.gz
+S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00JRB41.DNase.hotspot_v3.20141014.bed.gz
+S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ48.DNase.hotspot_v3.20130819.bed.gz
+S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00JS941.DNase.hotspot_v3.20141014.bed.gz
+S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ4A.DNase.hotspot_v3.20130819.bed.gz
+bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed.gz
+S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS/S005FH41.DNase.hotspot_v3.20130819.bed.gz
+bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed.gz
+S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00BXV41.DNase.hotspot_v3.20141014.bed.gz
+S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00BYT41.DNase.hotspot_v3.20141014.bed.gz
diff --git a/database/encode.decode b/database/encode.decode
new file mode 100644
index 0000000..3e67025
--- /dev/null
+++ b/database/encode.decode
@@ -0,0 +1,126 @@
+file lab datatype cell tissue shortcell individual acc url
+A549-all.twopass.merge150.wgt10.zgt2.wig Combined DHS A549 Epithelium A549 NA "GSM816649,GSM736580,GSM736506" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/A549-all.twopass.merge150.wgt10.zgt2.wig
+Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Adult_CD4+ Blood Adult_CD4+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig UW DHS AG04449 Skin AG04449 NA "GSM736562,GSM736590" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig
+AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig UW DHS AG04450 Lung AG04450 NA "GSM736514,GSM736563" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig
+AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig UW DHS AG09309 Skin AG09309 NA "GSM736551,GSM736616" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig
+AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig UW DHS AG09319 Gingival AG09319 NA "GSM736531,GSM736619" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig
+AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig UW DHS AG10803 Skin AG10803 NA "GSM736598,GSM736633" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig
+AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig UW DHS AoAF Blood vessel AoAF NA "GSM736583,GSM736505" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig
+BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig UW DHS BE2_C Brain BE2_C NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig
+BJ-DS10081.twopass.merge150.wgt10.zgt2.wig UW DHS BJ Skin BJ NA "GSM736518,GSM736596" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BJ-DS10081.twopass.merge150.wgt10.zgt2.wig
+CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig UW DHS Caco-2 Colon Caco-2 NA "GSM736500,GSM736587" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig
+CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD14+ Blood CD14+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig
+CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD20+ Blood CD20+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig
+CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD34+ Blood CD34+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig
+CMK-DS12393.twopass.merge150.wgt10.zgt2.wig UW DHS CMK Blood CMK NA GSM736607 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CMK-DS12393.twopass.merge150.wgt10.zgt2.wig
+E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS E_myoblast Muscle E_myoblast NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig UW DHS GM06990 Blood GM06990 NA "GSM736558,GSM736635" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig
+GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig UW DHS GM12864 Blood GM12864 NA GSM736525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig
+GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig UW DHS GM12865 Blood GM12865 NA "GSM736512,GSM736561" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig
+GM12878-all.twopass.merge150.wgt10.zgt2.wig Combined DHS GM12878 Blood GM12878 NA "GSM816665,GSM736496,GSM736620" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12878-all.twopass.merge150.wgt10.zgt2.wig
+HAc-DS14765.twopass.merge150.wgt10.zgt2.wig UW DHS HAc Cerebellar HAc NA "GSM736586,GSM736538" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAc-DS14765.twopass.merge150.wgt10.zgt2.wig
+HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig UW DHS HAEpiC Epithelium HAEpiC NA "GSM736631,GSM736606" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig
+HAh-DS15192.twopass.merge150.wgt10.zgt2.wig UW DHS HA-h Brain hippocampus HA-h NA "GSM736594,GSM736535" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAh-DS15192.twopass.merge150.wgt10.zgt2.wig
+HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig UW DHS HA-sp Spinal cord HA-sp NA "GSM736537,GSM736625" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig
+HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig UW DHS HBMEC Blood vessel HBMEC NA "GSM736509,GSM736554" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig
+HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig UW DHS HCFaa Heart HCFaa NA "GSM736494,GSM736601" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig
+HCF-DS12501.twopass.merge150.wgt10.zgt2.wig UW DHS HCF Heart HCF NA "GSM736568,GSM736540" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCF-DS12501.twopass.merge150.wgt10.zgt2.wig
+HCM-DS12599.twopass.merge150.wgt10.zgt2.wig UW DHS HCM Heart HCM NA "GSM736516,GSM736504" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCM-DS12599.twopass.merge150.wgt10.zgt2.wig
+HConF-DS11642.twopass.merge150.wgt10.zgt2.wig UW DHS HConF Eye HConF NA "GSM736547,GSM736515" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HConF-DS11642.twopass.merge150.wgt10.zgt2.wig
+HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig UW DHS HCPEpiC Epithelium HCPEpiC NA "GSM736569,GSM736597" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig
+HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig UW DHS HCT-116 Colon HCT-116 NA "GSM736600,GSM736493" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig
+HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig UW DHS HEEpiC Epithelium HEEpiC NA "GSM736585,GSM736532" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig
+Hela-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Hela-all.twopass.merge150.wgt10.zgt2.wig
+HepG2-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HepG2 Liver HepG2 NA "GSM816662,GSM736637,GSM736639" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HepG2-all.twopass.merge150.wgt10.zgt2.wig
+HESC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HESC ES Cell HESC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HESC-all.twopass.merge150.wgt10.zgt2.wig
+hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig UW DHS hESCT0 ES Cell hESCT0 NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig
+HFF-DS15115.twopass.merge150.wgt10.zgt2.wig UW DHS HFF Foreskin HFF NA "GSM736602,GSM736572" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF-DS15115.twopass.merge150.wgt10.zgt2.wig
+HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig UW DHS HFF-Myc Foreskin HFF-Myc NA "GSM736524,GSM736605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig
+HGF-DS11752.twopass.merge150.wgt10.zgt2.wig UW DHS HGF Gingival HGF NA "GSM736579,GSM736576" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HGF-DS11752.twopass.merge150.wgt10.zgt2.wig
+HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig UW DHS HIPEpiC Epithelium HIPEpiC NA "GSM736589,GSM736615" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig
+HL60-DS11809.twopass.merge150.wgt10.zgt2.wig UW DHS HL-60 Blood HL-60 NA "GSM736626,GSM736595" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HL60-DS11809.twopass.merge150.wgt10.zgt2.wig
+HMEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HMEC Breast HMEC NA "GSM816669,GSM736634,GSM736552" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMEC-all.twopass.merge150.wgt10.zgt2.wig
+HMF-DS13363.twopass.merge150.wgt10.zgt2.wig UW DHS HMF Breast HMF NA "GSM736628,GSM736541" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMF-DS13363.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dAd Blood vessel HMVEC-dAd NA "GSM1024745,GSM1024747" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Ad Blood vessel HMVEC-dBl-Ad NA "GSM736609,GSM736523" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Neo Blood vessel HMVEC-dBl-Neo NA "GSM736571,GSM736521" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Ad Blood vessel HMVEC-dLy-Ad NA "GSM736599,GSM736591" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Neo Blood vessel HMVEC-dLy-Neo NA "GSM736577,GSM736573" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig
+HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dNeo Blood vessel HMVEC-dNeo NA "GSM736611,GSM736624" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig
+HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LBl Blood vessel HMVEC-LBl NA "GSM736542,GSM736511" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig
+HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LLy Blood vessel HMVEC-LLy NA "GSM736507,GSM736627" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig
+HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig UW DHS HNPCEpiC Epithelium HNPCEpiC NA "GSM736621,GSM736550" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig
+HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HPAEC Blood vessel HPAEC NA GSM1024763 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig
+HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig UW DHS HPAF Blood vessel HPAF NA "GSM736555,GSM736614" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig
+HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig UW DHS HPdLF Epithelium HPdLF NA "GSM736632,GSM736528" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig
+HPF-DS13390.twopass.merge150.wgt10.zgt2.wig UW DHS HPF Lung HPF NA "GSM736574,GSM736503" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPF-DS13390.twopass.merge150.wgt10.zgt2.wig
+HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig UW DHS HRCEpiC Epithelium HRCEpiC NA "GSM736549,GSM736557" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig
+HRE-DS10641.twopass.merge150.wgt10.zgt2.wig UW DHS HRE Epithelium HRE NA "GSM736527,GSM736548" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRE-DS10641.twopass.merge150.wgt10.zgt2.wig
+HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig UW DHS HRGEC Kidney HRGEC NA "GSM736499,GSM736618" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig
+HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig UW DHS HRPEpiC Epithelium HRPEpiC NA "GSM736630,GSM736623" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig
+HSMM-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM-all.twopass.merge150.wgt10.zgt2.wig
+HSMM_D-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM_D-all.twopass.merge150.wgt10.zgt2.wig
+hTH1-all.twopass.merge150.wgt10.zgt2.wig Combined DHS Th1 Blood Th1 NA "GSM736592,GSM1024760" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH1-all.twopass.merge150.wgt10.zgt2.wig
+hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig UW DHS Th2 Blood Th2 NA "GSM736502,GSM1024792" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig
+HUVEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HUVEC Blood vessel HUVEC NA "GSM816646,GSM736575,GSM736533" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HUVEC-all.twopass.merge150.wgt10.zgt2.wig
+HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig UW DHS HVMF Connective HVMF NA "GSM736534,GSM736491" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig
+Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig UW DHS Jurkat Blood Jurkat NA "GSM736501,GSM736492" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig
+K562-all.twopass.merge150.wgt10.zgt2.wig Combined DHS K562 Blood K562 NA "GSM816655,GSM1008602,GSM1008567,GSM1008601,GSM1008558,GSM1008580,GSM736629,GSM736566" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/K562-all.twopass.merge150.wgt10.zgt2.wig
+LNCap-all.twopass.merge150.wgt10.zgt2.wig Combined DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/LNCap-all.twopass.merge150.wgt10.zgt2.wig
+MCF7-all.twopass.merge150.wgt10.zgt2.wig Combined DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/MCF7-all.twopass.merge150.wgt10.zgt2.wig
+NB4-DS12543.twopass.merge150.wgt10.zgt2.wig UW DHS NB4 Blood NB4 NA "GSM736604,GSM736529" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NB4-DS12543.twopass.merge150.wgt10.zgt2.wig
+NHA-DS12800.twopass.merge150.wgt10.zgt2.wig UW DHS NH-A Nervous NH-A NA "GSM736544,GSM736584" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHA-DS12800.twopass.merge150.wgt10.zgt2.wig
+NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-Ad Skin NHDF-Ad NA "GSM736567,GSM736520" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig
+NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-neo Skin NHDF-neo NA "GSM736498,GSM736546" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig
+NHEK-all.twopass.merge150.wgt10.zgt2.wig Combined DHS NHEK Skin NHEK NA "GSM816635,GSM736545,GSM736556" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHEK-all.twopass.merge150.wgt10.zgt2.wig
+NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig UW DHS NHLF Lung NHLF NA "GSM736612,GSM736536" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig
+NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS NT2-D1 Testis NT2-D1 NA "GSM1024751,GSM1024795" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig
+PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig UW DHS PANC-1 Pancreas PANC-1 NA "GSM736517,GSM736519" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig
+PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS PrEC Prostate PrEC NA "GSM1024742,GSM1024743" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig
+RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig UW DHS RPTEC Epithelium RPTEC NA "GSM736543,GSM736539" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig
+RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS RWPE1 Prostate RWPE1 NA GSM1008595 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig UW DHS SAEC Epithelium SAEC NA "GSM736608,GSM736617" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig
+SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig UW DHS SKMC Muscle SKMC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig
+SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-MC Brain SK-N-MC NA "GSM736522,GSM736570" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig
+SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-SH Brain SK-N-SH NA GSM1008585 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig
+WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig UW DHS WERI-Rb-1 Eye WERI-Rb-1 NA "GSM736495,GSM736636" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS 8988T Liver 8988T NA GSM816667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS AoSMC Blood vessel AoSMC NA GSM816638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Chorion Fetal membrane Chorion NA GSM816628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS CLL Blood CLL NA GSM816664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Fibrobl Skin Fibrobl NA GSM816652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS FibroP Skin FibroP NA GSM816626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Gliobla Brain Gliobla NA GSM816668 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12891 Blood GM12891 NA GSM816656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12892 Blood GM12892 NA GSM816657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM18507 Blood GM18507 NA GSM816653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19238 Blood GM19238 NA GSM816658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19239 Blood GM19239 NA GSM816659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19240 Blood GM19240 NA GSM816648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS H9ES ES Cell H9ES NA GSM816629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Hepatocytes Liver Hepatocytes NA GSM816663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HPDE6-E6E7 Pancreatic duct HPDE6-E6E7 NA GSM816639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HTR8svn Blastula HTR8svn NA GSM816644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7.5 Liver Huh-7.5 NA GSM816671 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7 Liver Huh-7 NA GSM816641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS iPS IPS iPS NA GSM816642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Medullo Brain Medullo NA GSM816636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Melano Skin Melano NA GSM816631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Myometr Myometrium Myometr NA GSM816630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Osteobl Bone Osteobl NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIsletD Pancreas PanIsletD NA GSM816666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIslets Pancreas PanIslets NA GSM816660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS pHTE Epithelium pHTE NA GSM816647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS ProgFib Skin ProgFib NA GSM816661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Stellate Liver Stellate NA GSM816672 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS T-47D Breast T-47D NA "GSM816673,GSM1008576,GSM1024762,GSM1024761" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig
+WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig
+WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig
\ No newline at end of file
diff --git a/database/erc.decode b/database/erc.decode
new file mode 100644
index 0000000..bd80775
--- /dev/null
+++ b/database/erc.decode
@@ -0,0 +1,300 @@
+file lab datatype cell tissue shortcell individual acc url
+UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753973 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753974 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01689+ Blood CD14 RO_01689+ GSM701503 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01701+ Blood CD14 RO_01701+ GSM701541 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01679+ Blood CD19 RO_01679+ GSM701492 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01689+ Blood CD19 RO_01689+ GSM701493 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01701+ Blood CD19 RO_01701+ GSM701507 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD20_Primary_Cells.RO_01778+ Blood CD20 RO_01778+ GSM701500 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB1_1-3-2011+ Blood CD3 CB1_1-3-2011+ GSM701525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB6_1-4-2011+ Blood CD3 CB6_1-4-2011+ GSM701526 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz
+UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.RO_01679+ Blood CD3 RO_01679+ GSM665837 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz
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+UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530665 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz
+UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz
+UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.11 IPS cell iPS_DF_19.11 NA GSM665801 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz
+UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.7 IPS cell iPS_DF_19.7 NA GSM665800 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz
+UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_4.7 IPS cell iPS_DF_4.7 NA GSM665803 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz
+UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_6.9 IPS cell iPS_DF_6.9 NA GSM665802 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_00738+ Blood CD34_Mobilised; RO_00738+ GSM530664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01480+ Blood CD34_Mobilised; RO_01480+ GSM530658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01492+ Blood CD34_Mobilised; RO_01492+ GSM530659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01492+ Blood CD34_Mobilised; RO_01492+ GSM595919 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01508+ Blood CD34_Mobilised; RO_01508+ GSM493386 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01517+ Blood CD34_Mobilised; RO_01517+ GSM595917 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01520+ Blood CD34_Mobilised; RO_01520+ GSM530660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01527+ Blood CD34_Mobilised; RO_01527+ GSM493387 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01535+ Blood CD34_Mobilised; RO_01535+ GSM493384 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01535+ Blood CD34_Mobilised; RO_01535+ GSM595918 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01536+ Blood CD34_Mobilised; RO_01536+ GSM530652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12339.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01549+ Blood CD34_Mobilised; RO_01549+ GSM530657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01562.DS13196.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01562+ Blood CD34_Mobilised; RO_01562+ GSM530663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01562.DS13196.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01701.DS17112.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01701+ Blood CD34_Mobilised; RO_01701+ GSM774208 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01701.DS17112.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS16955.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD4_Primary_Cells.RO_01679+ Blood CD4_Mobilised; RO_01679+ GSM701489 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS16955.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17175.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD4_Primary_Cells.RO_01701+ Blood CD4_Mobilised; RO_01701+ GSM701491 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17175.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD56_Primary_Cells.ChromatinAccessibility.RO_01689.DS16376.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD56_Primary_Cells.RO_01689+ Blood CD56_Mobilised; RO_01689+ GSM665820 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD56_Primary_Cells.ChromatinAccessibility.RO_01689.DS16376.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Mobilized_CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS16962.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD8_Primary_Cells.RO_01679+ Blood CD8_Mobilised; RO_01679+ GSM817160 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS16962.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18224.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Fibroblast_Primary_Cells.skin01 Fibroblast Penis_Foreskin_Fibroblast skin01 GSM774240 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18224.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18229.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Fibroblast_Primary_Cells.skin01 Fibroblast Penis_Foreskin_Fibroblast skin01 GSM774241 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin01.DS18229.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Fibroblast_Primary_Cells.skin02 Fibroblast Penis_Foreskin_Fibroblast skin02 GSM817169 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18256.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Fibroblast_Primary_Cells.skin02 Fibroblast Penis_Foreskin_Fibroblast skin02 GSM817170 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18256.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18692.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Keratinocyte_Primary_Cells.skin01 Skin Penis_Foreskin_Keratinocyte skin01 GSM817194 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18692.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Keratinocyte_Primary_Cells.skin01 Skin Penis_Foreskin_Keratinocyte skin01 GSM817195 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18714.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Keratinocyte_Primary_Cells.skin02 Skin Penis_Foreskin_Keratinocyte skin02 GSM817196 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18714.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18718.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Keratinocyte_Primary_Cells.skin02 Skin Penis_Foreskin_Keratinocyte skin02 GSM817197 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18718.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18590.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Melanocyte_Primary_Cells.skin01 Skin Penis_Foreskin_Melanocyte skin01 GSM774243 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18590.twopass.merge150.wgt10.zgt2.wig.gz
+UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Penis_Foreskin_Melanocyte_Primary_Cells.skin01 Skin Penis_Foreskin_Melanocyte skin01 GSM774244 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.twopass.merge150.wgt10.zgt2.wig.gz
\ No newline at end of file
diff --git a/database/erc2-H3-all.decode b/database/erc2-H3-all.decode
new file mode 100644
index 0000000..ded135b
--- /dev/null
+++ b/database/erc2-H3-all.decode
@@ -0,0 +1,196 @@
+file lab datatype cell tissue shortcell individual acc url
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+E004-H3K27me3.broadPeak UW H3K27me3 E004 H1 BMP4 Derived Mesendoderm Cultured Cells ES Cell E004 H1 BMP4 Derived Mesendoderm Cultured Cells NA E004 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E004-H3K27me3.broadPeak.gz
+E005-H3K27me3.broadPeak UW H3K27me3 E005 H1 BMP4 Derived Trophoblast Cultured Cells ES Cell E005 H1 BMP4 Derived Trophoblast Cultured Cells NA E005 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E005-H3K27me3.broadPeak.gz
+E006-H3K27me3.broadPeak UW H3K27me3 E006 H1 Derived Mesenchymal Stem Cells ES Cell E006 H1 Derived Mesenchymal Stem Cells NA E006 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E006-H3K27me3.broadPeak.gz
+E007-H3K27me3.broadPeak UW H3K27me3 E007 H1 Derived Neuronal Progenitor Cultured Cells ES Cell E007 H1 Derived Neuronal Progenitor Cultured Cells NA E007 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E007-H3K27me3.broadPeak.gz
+E008-H3K27me3.broadPeak UW H3K27me3 E008 H9 Cells ES Cell E008 H9 Cells NA E008 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E008-H3K27me3.broadPeak.gz
+E017-H3K27me3.broadPeak UW H3K27me3 E017 IMR90 fetal lung fibroblasts Cell Line Lung E017 IMR90 fetal lung fibroblasts Cell Line NA E017 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E017-H3K27me3.broadPeak.gz
+E021-H3K27me3.broadPeak UW H3K27me3 E021 iPS DF 6.9 Cells IPS cell E021 iPS DF 6.9 Cells NA E021 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E021-H3K27me3.broadPeak.gz
+E022-H3K27me3.broadPeak UW H3K27me3 E022 iPS DF 19.11 Cells IPS cell E022 iPS DF 19.11 Cells NA E022 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E022-H3K27me3.broadPeak.gz
+E028-H3K27me3.broadPeak UW H3K27me3 E028 Breast variant Human Mammary Epithelial Cells Breast E028 Breast variant Human Mammary Epithelial Cells NA E028 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E028-H3K27me3.broadPeak.gz
+E029-H3K27me3.broadPeak UW H3K27me3 E029 Primary monocytes from peripheral blood Blood E029 Primary monocytes from peripheral blood NA E029 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E029-H3K27me3.broadPeak.gz
+E032-H3K27me3.broadPeak UW H3K27me3 E032 Primary B cells from peripheral blood Blood E032 Primary B cells from peripheral blood NA E032 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E032-H3K27me3.broadPeak.gz
+E033-H3K27me3.broadPeak UW H3K27me3 E033 Primary T cells from cord blood Blood E033 Primary T cells from cord blood NA E033 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E033-H3K27me3.broadPeak.gz
+E034-H3K27me3.broadPeak UW H3K27me3 E034 Primary T cells from peripheral blood Blood E034 Primary T cells from peripheral blood NA E034 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E034-H3K27me3.broadPeak.gz
+E046-H3K27me3.broadPeak UW H3K27me3 E046 Primary Natural Killer cells from peripheral Blood E046 Primary Natural Killer cells from peripheral NA E046 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E046-H3K27me3.broadPeak.gz
+E050-H3K27me3.broadPeak UW H3K27me3 E050 Primary hematopoietic stem cells G-CSF-mobili Blood E050 Primary hematopoietic stem cells G-CSF-mobili NA E050 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E050-H3K27me3.broadPeak.gz
+E051-H3K27me3.broadPeak UW H3K27me3 E051 Primary hematopoietic stem cells G-CSF-mobili Blood E051 Primary hematopoietic stem cells G-CSF-mobili NA E051 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E051-H3K27me3.broadPeak.gz
+E055-H3K27me3.broadPeak UW H3K27me3 E055 Foreskin Fibroblast Primary Cells skin01 Skin E055 Foreskin Fibroblast Primary Cells skin01 NA E055 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E055-H3K27me3.broadPeak.gz
+E056-H3K27me3.broadPeak UW H3K27me3 E056 Foreskin Fibroblast Primary Cells skin02 Skin E056 Foreskin Fibroblast Primary Cells skin02 NA E056 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E056-H3K27me3.broadPeak.gz
+E057-H3K27me3.broadPeak UW H3K27me3 E057 Foreskin Keratinocyte Primary Cells skin02 Skin E057 Foreskin Keratinocyte Primary Cells skin02 NA E057 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E057-H3K27me3.broadPeak.gz
+E059-H3K27me3.broadPeak UW H3K27me3 E059 Foreskin Melanocyte Primary Cells skin01 Skin E059 Foreskin Melanocyte Primary Cells skin01 NA E059 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E059-H3K27me3.broadPeak.gz
+E080-H3K27me3.broadPeak UW H3K27me3 E080 Fetal Adrenal Gland Fetal Adrenal Gland E080 Fetal Adrenal Gland NA E080 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E080-H3K27me3.broadPeak.gz
+E081-H3K27me3.broadPeak UW H3K27me3 E081 Fetal Brain Male Fetal Brain E081 Fetal Brain Male NA E081 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E081-H3K27me3.broadPeak.gz
+E082-H3K27me3.broadPeak UW H3K27me3 E082 Fetal Brain Female Fetal Brain E082 Fetal Brain Female NA E082 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E082-H3K27me3.broadPeak.gz
+E083-H3K27me3.broadPeak UW H3K27me3 E083 Fetal Heart Fetal Heart E083 Fetal Heart NA E083 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E083-H3K27me3.broadPeak.gz
+E084-H3K27me3.broadPeak UW H3K27me3 E084 Fetal Intestine Large Fetal Intestine Large E084 Fetal Intestine Large NA E084 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E084-H3K27me3.broadPeak.gz
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\ No newline at end of file
diff --git a/database/erc2-H3K27me3.decode b/database/erc2-H3K27me3.decode
new file mode 100644
index 0000000..bab337e
--- /dev/null
+++ b/database/erc2-H3K27me3.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
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\ No newline at end of file
diff --git a/database/erc2-H3K36me3.decode b/database/erc2-H3K36me3.decode
new file mode 100644
index 0000000..955eb95
--- /dev/null
+++ b/database/erc2-H3K36me3.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
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\ No newline at end of file
diff --git a/database/erc2-H3K4me1.decode b/database/erc2-H3K4me1.decode
new file mode 100644
index 0000000..e10db0f
--- /dev/null
+++ b/database/erc2-H3K4me1.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
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\ No newline at end of file
diff --git a/database/erc2-H3K4me3.decode b/database/erc2-H3K4me3.decode
new file mode 100644
index 0000000..3c9db1b
--- /dev/null
+++ b/database/erc2-H3K4me3.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
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\ No newline at end of file
diff --git a/database/erc2-H3K9me3.decode b/database/erc2-H3K9me3.decode
new file mode 100644
index 0000000..7946898
--- /dev/null
+++ b/database/erc2-H3K9me3.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
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+E080-H3K9me3.broadPeak UW H3K9me3 E080 Fetal Adrenal Gland Fetal Adrenal Gland E080 Fetal Adrenal Gland NA E080 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E080-H3K9me3.broadPeak.gz
+E081-H3K9me3.broadPeak UW H3K9me3 E081 Fetal Brain Male Fetal Brain E081 Fetal Brain Male NA E081 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E081-H3K9me3.broadPeak.gz
+E082-H3K9me3.broadPeak UW H3K9me3 E082 Fetal Brain Female Fetal Brain E082 Fetal Brain Female NA E082 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E082-H3K9me3.broadPeak.gz
+E083-H3K9me3.broadPeak UW H3K9me3 E083 Fetal Heart Fetal Heart E083 Fetal Heart NA E083 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E083-H3K9me3.broadPeak.gz
+E084-H3K9me3.broadPeak UW H3K9me3 E084 Fetal Intestine Large Fetal Intestine Large E084 Fetal Intestine Large NA E084 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E084-H3K9me3.broadPeak.gz
+E085-H3K9me3.broadPeak UW H3K9me3 E085 Fetal Intestine Small Feta Intestine Small E085 Fetal Intestine Small NA E085 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E085-H3K9me3.broadPeak.gz
+E086-H3K9me3.broadPeak UW H3K9me3 E086 Fetal Kidney Fetal Kidney E086 Fetal Kidney NA E086 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E086-H3K9me3.broadPeak.gz
+E088-H3K9me3.broadPeak UW H3K9me3 E088 Fetal Lung Fetal Lung E088 Fetal Lung NA E088 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E088-H3K9me3.broadPeak.gz
+E089-H3K9me3.broadPeak UW H3K9me3 E089 Fetal Muscle Trunk Fetal Muscle Trunk E089 Fetal Muscle Trunk NA E089 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E089-H3K9me3.broadPeak.gz
+E090-H3K9me3.broadPeak UW H3K9me3 E090 Fetal Muscle Leg Fetal Muscle Leg E090 Fetal Muscle Leg NA E090 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E090-H3K9me3.broadPeak.gz
+E091-H3K9me3.broadPeak UW H3K9me3 E091 Placenta Placenta E091 Placenta NA E091 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E091-H3K9me3.broadPeak.gz
+E092-H3K9me3.broadPeak UW H3K9me3 E092 Fetal Stomach Fetal Stomach E092 Fetal Stomach NA E092 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E092-H3K9me3.broadPeak.gz
+E093-H3K9me3.broadPeak UW H3K9me3 E093 Fetal Thymus Fetal Thymus E093 Fetal Thymus NA E093 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E093-H3K9me3.broadPeak.gz
+E094-H3K9me3.broadPeak UW H3K9me3 E094 Gastric Gastric E094 Gastric NA E094 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E094-H3K9me3.broadPeak.gz
+E097-H3K9me3.broadPeak UW H3K9me3 E097 Ovary Ovary E097 Ovary NA E097 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E097-H3K9me3.broadPeak.gz
+E098-H3K9me3.broadPeak UW H3K9me3 E098 Pancreas Pancreas E098 Pancreas NA E098 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E098-H3K9me3.broadPeak.gz
+E100-H3K9me3.broadPeak UW H3K9me3 E100 Psoas Muscle Psoas Muscle E100 Psoas Muscle NA E100 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E100-H3K9me3.broadPeak.gz
+E109-H3K9me3.broadPeak UW H3K9me3 E109 Small Intestine Small Intestine E109 Small Intestine NA E109 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/E109-H3K9me3.broadPeak.gz
\ No newline at end of file
diff --git a/database/erc2.decode b/database/erc2.decode
new file mode 100644
index 0000000..5a42cc7
--- /dev/null
+++ b/database/erc2.decode
@@ -0,0 +1,40 @@
+file lab datatype cell tissue shortcell individual acc url
+E003-DNase.hotspot.fdr0.01.broad.bed UW DHS E003 H1 Cells ES Cell E003 H1 Cells NA E003 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E003-DNase.hotspot.fdr0.01.broad.bed.gz
+E004-DNase.hotspot.fdr0.01.broad.bed UW DHS E004 H1 BMP4 Derived Mesendoderm Cultured Cells ES Cell E004 H1 BMP4 Derived Mesendoderm Cultured Cells NA E004 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E004-DNase.hotspot.fdr0.01.broad.bed.gz
+E005-DNase.hotspot.fdr0.01.broad.bed UW DHS E005 H1 BMP4 Derived Trophoblast Cultured Cells ES Cell E005 H1 BMP4 Derived Trophoblast Cultured Cells NA E005 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E005-DNase.hotspot.fdr0.01.broad.bed.gz
+E006-DNase.hotspot.fdr0.01.broad.bed UW DHS E006 H1 Derived Mesenchymal Stem Cells ES Cell E006 H1 Derived Mesenchymal Stem Cells NA E006 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E006-DNase.hotspot.fdr0.01.broad.bed.gz
+E007-DNase.hotspot.fdr0.01.broad.bed UW DHS E007 H1 Derived Neuronal Progenitor Cultured Cells ES Cell E007 H1 Derived Neuronal Progenitor Cultured Cells NA E007 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E007-DNase.hotspot.fdr0.01.broad.bed.gz
+E008-DNase.hotspot.fdr0.01.broad.bed UW DHS E008 H9 Cells ES Cell E008 H9 Cells NA E008 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E008-DNase.hotspot.fdr0.01.broad.bed.gz
+E017-DNase.hotspot.fdr0.01.broad.bed UW DHS E017 IMR90 fetal lung fibroblasts Cell Line Lung E017 IMR90 fetal lung fibroblasts Cell Line NA E017 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E017-DNase.hotspot.fdr0.01.broad.bed.gz
+E021-DNase.hotspot.fdr0.01.broad.bed UW DHS E021 iPS DF 6.9 Cells IPS cell E021 iPS DF 6.9 Cells NA E021 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E021-DNase.hotspot.fdr0.01.broad.bed.gz
+E022-DNase.hotspot.fdr0.01.broad.bed UW DHS E022 iPS DF 19.11 Cells IPS cell E022 iPS DF 19.11 Cells NA E022 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E022-DNase.hotspot.fdr0.01.broad.bed.gz
+E028-DNase.hotspot.fdr0.01.broad.bed UW DHS E028 Breast variant Human Mammary Epithelial Cells Breast E028 Breast variant Human Mammary Epithelial Cells NA E028 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E028-DNase.hotspot.fdr0.01.broad.bed.gz
+E029-DNase.hotspot.fdr0.01.broad.bed UW DHS E029 Primary monocytes from peripheral blood Blood E029 Primary monocytes from peripheral blood NA E029 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E029-DNase.hotspot.fdr0.01.broad.bed.gz
+E032-DNase.hotspot.fdr0.01.broad.bed UW DHS E032 Primary B cells from peripheral blood Blood E032 Primary B cells from peripheral blood NA E032 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E032-DNase.hotspot.fdr0.01.broad.bed.gz
+E033-DNase.hotspot.fdr0.01.broad.bed UW DHS E033 Primary T cells from cord blood Blood E033 Primary T cells from cord blood NA E033 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E033-DNase.hotspot.fdr0.01.broad.bed.gz
+E034-DNase.hotspot.fdr0.01.broad.bed UW DHS E034 Primary T cells from peripheral blood Blood E034 Primary T cells from peripheral blood NA E034 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E034-DNase.hotspot.fdr0.01.broad.bed.gz
+E046-DNase.hotspot.fdr0.01.broad.bed UW DHS E046 Primary Natural Killer cells from peripheral Blood E046 Primary Natural Killer cells from peripheral NA E046 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E046-DNase.hotspot.fdr0.01.broad.bed.gz
+E050-DNase.hotspot.fdr0.01.broad.bed UW DHS E050 Primary hematopoietic stem cells G-CSF-mobili Blood E050 Primary hematopoietic stem cells G-CSF-mobili NA E050 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E050-DNase.hotspot.fdr0.01.broad.bed.gz
+E051-DNase.hotspot.fdr0.01.broad.bed UW DHS E051 Primary hematopoietic stem cells G-CSF-mobili Blood E051 Primary hematopoietic stem cells G-CSF-mobili NA E051 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E051-DNase.hotspot.fdr0.01.broad.bed.gz
+E055-DNase.hotspot.fdr0.01.broad.bed UW DHS E055 Foreskin Fibroblast Primary Cells skin01 Skin E055 Foreskin Fibroblast Primary Cells skin01 NA E055 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E055-DNase.hotspot.fdr0.01.broad.bed.gz
+E056-DNase.hotspot.fdr0.01.broad.bed UW DHS E056 Foreskin Fibroblast Primary Cells skin02 Skin E056 Foreskin Fibroblast Primary Cells skin02 NA E056 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E056-DNase.hotspot.fdr0.01.broad.bed.gz
+E057-DNase.hotspot.fdr0.01.broad.bed UW DHS E057 Foreskin Keratinocyte Primary Cells skin02 Skin E057 Foreskin Keratinocyte Primary Cells skin02 NA E057 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E057-DNase.hotspot.fdr0.01.broad.bed.gz
+E059-DNase.hotspot.fdr0.01.broad.bed UW DHS E059 Foreskin Melanocyte Primary Cells skin01 Skin E059 Foreskin Melanocyte Primary Cells skin01 NA E059 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E059-DNase.hotspot.fdr0.01.broad.bed.gz
+E080-DNase.hotspot.fdr0.01.broad.bed UW DHS E080 Fetal Adrenal Gland Fetal Adrenal Gland E080 Fetal Adrenal Gland NA E080 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E080-DNase.hotspot.fdr0.01.broad.bed.gz
+E081-DNase.hotspot.fdr0.01.broad.bed UW DHS E081 Fetal Brain Male Fetal Brain E081 Fetal Brain Male NA E081 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E081-DNase.hotspot.fdr0.01.broad.bed.gz
+E082-DNase.hotspot.fdr0.01.broad.bed UW DHS E082 Fetal Brain Female Fetal Brain E082 Fetal Brain Female NA E082 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E082-DNase.hotspot.fdr0.01.broad.bed.gz
+E083-DNase.hotspot.fdr0.01.broad.bed UW DHS E083 Fetal Heart Fetal Heart E083 Fetal Heart NA E083 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E083-DNase.hotspot.fdr0.01.broad.bed.gz
+E084-DNase.hotspot.fdr0.01.broad.bed UW DHS E084 Fetal Intestine Large Fetal Intestine Large E084 Fetal Intestine Large NA E084 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E084-DNase.hotspot.fdr0.01.broad.bed.gz
+E085-DNase.hotspot.fdr0.01.broad.bed UW DHS E085 Fetal Intestine Small Feta Intestine Small E085 Fetal Intestine Small NA E085 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E085-DNase.hotspot.fdr0.01.broad.bed.gz
+E086-DNase.hotspot.fdr0.01.broad.bed UW DHS E086 Fetal Kidney Fetal Kidney E086 Fetal Kidney NA E086 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E086-DNase.hotspot.fdr0.01.broad.bed.gz
+E088-DNase.hotspot.fdr0.01.broad.bed UW DHS E088 Fetal Lung Fetal Lung E088 Fetal Lung NA E088 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E088-DNase.hotspot.fdr0.01.broad.bed.gz
+E089-DNase.hotspot.fdr0.01.broad.bed UW DHS E089 Fetal Muscle Trunk Fetal Muscle Trunk E089 Fetal Muscle Trunk NA E089 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E089-DNase.hotspot.fdr0.01.broad.bed.gz
+E090-DNase.hotspot.fdr0.01.broad.bed UW DHS E090 Fetal Muscle Leg Fetal Muscle Leg E090 Fetal Muscle Leg NA E090 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E090-DNase.hotspot.fdr0.01.broad.bed.gz
+E091-DNase.hotspot.fdr0.01.broad.bed UW DHS E091 Placenta Placenta E091 Placenta NA E091 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E091-DNase.hotspot.fdr0.01.broad.bed.gz
+E092-DNase.hotspot.fdr0.01.broad.bed UW DHS E092 Fetal Stomach Fetal Stomach E092 Fetal Stomach NA E092 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E092-DNase.hotspot.fdr0.01.broad.bed.gz
+E093-DNase.hotspot.fdr0.01.broad.bed UW DHS E093 Fetal Thymus Fetal Thymus E093 Fetal Thymus NA E093 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E093-DNase.hotspot.fdr0.01.broad.bed.gz
+E094-DNase.hotspot.fdr0.01.broad.bed UW DHS E094 Gastric Gastric E094 Gastric NA E094 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E094-DNase.hotspot.fdr0.01.broad.bed.gz
+E097-DNase.hotspot.fdr0.01.broad.bed UW DHS E097 Ovary Ovary E097 Ovary NA E097 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E097-DNase.hotspot.fdr0.01.broad.bed.gz
+E098-DNase.hotspot.fdr0.01.broad.bed UW DHS E098 Pancreas Pancreas E098 Pancreas NA E098 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E098-DNase.hotspot.fdr0.01.broad.bed.gz
+E100-DNase.hotspot.fdr0.01.broad.bed UW DHS E100 Psoas Muscle Psoas Muscle E100 Psoas Muscle NA E100 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E100-DNase.hotspot.fdr0.01.broad.bed.gz
+E109-DNase.hotspot.fdr0.01.broad.bed UW DHS E109 Small Intestine Small Intestine E109 Small Intestine NA E109 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E109-DNase.hotspot.fdr0.01.broad.bed.gz
\ No newline at end of file
diff --git a/database/init_db.pl b/database/init_db.pl
new file mode 100644
index 0000000..7dc4a81
--- /dev/null
+++ b/database/init_db.pl
@@ -0,0 +1,112 @@
+#! /usr/bin/env perl
+use strict;
+use warnings;
+
+use DBI;
+use Getopt::Long;
+
+my $db_dir = ".";
+my $db_name = "eforge_1.2.db";
+
+
+my $help;
+
+my $desc = qq{init_db.pl [--db_name $db_name] [--db_dir $db_dir]
+
+where:
+ --db_name is the name of the SQLite file [def: $db_name]
+ --db_dir is the location of the SQLite file [def: $db_dir]
+
+};
+
+GetOptions(
+ "help" => \$help,
+ "db_name=s" => \$db_name,
+ "db_dir=s" => \$db_dir,
+ );
+
+if ($help) {
+ print $desc;
+ exit(0);
+}
+
+my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name";
+my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr;
+
+
+$dbh->do("CREATE TABLE IF NOT EXISTS assembly (
+ assembly_id INTEGER PRIMARY KEY AUTOINCREMENT,
+ species_name,
+ assembly_name,
+ UNIQUE (species_name, assembly_name))");
+
+
+$dbh->do("CREATE TABLE IF NOT EXISTS array (
+ array_id INTEGER PRIMARY KEY AUTOINCREMENT,
+ array_tag UNIQUE,
+ array_name UNIQUE,
+ species_name)");
+$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping_info (
+ probe_mapping_id INTEGER PRIMARY KEY AUTOINCREMENT,
+ array_id INTEGER NOT NULL REFERENCES array(array_id),
+ assembly_id INTEGER NOT NULL,
+ url,
+ UNIQUE (array_id, assembly_id))");
+$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping (
+ probe_mapping_id INTEGER NOT NULL REFERENCES probe_mapping_info(probe_mapping_id),
+ probe_id,
+ chr_name,
+ position INTEGER,
+ UNIQUE (probe_mapping_id, probe_id))");
+$dbh->do("CREATE INDEX probe_mapping_idx1 on probe_mapping (position, chr_name)");
+
+
+$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter_info (
+ array_id INTEGER NOT NULL REFERENCES array(array_id),
+ description,
+ UNIQUE(array_id))");
+$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter (
+ proxy_filter_id INTEGER NOT NULL REFERENCES proxy_filter_info(proxy_filter_id),
+ probe_id,
+ proxy_probes,
+ UNIQUE (proxy_filter_id, probe_id))");
+
+
+$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation_info (
+ array_id INTEGER NOT NULL REFERENCES array(array_id),
+ gene_reference_name NOT NULL,
+ cgi_reference_name NOT NULL,
+ url,
+ UNIQUE(array_id))");
+$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation (
+ array_id INTEGER NOT NULL REFERENCES probe_annotation_info(array_id),
+ probe_id NOT NULL,
+ gene_group,
+ cgi_group,
+ UNIQUE (array_id, probe_id))");
+
+
+$dbh->do("CREATE TABLE IF NOT EXISTS dataset (
+ dataset_id INTEGER PRIMARY KEY AUTOINCREMENT,
+ dataset_tag UNIQUE,
+ dataset_name UNIQUE,
+ species_name)");
+$dbh->do("CREATE TABLE IF NOT EXISTS sample (
+ dataset_id INTEGER REFERENCES dataset(dataset_id),
+ sample_order INTEGER,
+ file,
+ lab,
+ datatype,
+ cell,
+ tissue,
+ shortcell,
+ individual,
+ acc,
+ url)");
+$dbh->do("CREATE TABLE IF NOT EXISTS probe_bitstring (
+ array_id INTEGER NOT NULL REFERENCES array(array_id),
+ probe_id INTEGER NOT NULL,
+ dataset_id INTEGER NOT NULL REFERENCES dataset(dataset_id),
+ sum INTEGER,
+ bit,
+ UNIQUE(array_id,probe_id,dataset_id))");
diff --git a/database/load_27k_array.pl b/database/load_27k_array.pl
new file mode 100644
index 0000000..c5e8011
--- /dev/null
+++ b/database/load_27k_array.pl
@@ -0,0 +1,346 @@
+#! /usr/bin/env perl
+use strict;
+use warnings;
+
+use Getopt::Long;
+use File::Spec qw(splitpath);
+use DBI;
+
+my $db_dir = ".";
+my $db_name = "eforge_1.2.db";
+my $array_tag = "27k";
+my $array_name = "Illumina Human 27k array (subset of 450k only)";
+my $species = "Homo sapiens";
+my $proxy_threshold = 1000;
+my $illumina27k_bpm_file = 'ftp://webdata:webdata@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation27/humanmethylation27_270596_v1-2.bpm';
+my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv';
+my $work_dir = ".";
+my $bedtools = "bedtools";
+
+my $help;
+
+my $desc = qq{load_27k_array.pl [options]
+
+DESCRIPTION:
+
+This script loads the subset of probe locations and annotations of the Illumina Human 27k
+methylation array that are shared with the 450k array into the eFORGE database.
+
+Note that you *must* load the arrays before loading the datasets. If you want to include new arrays
+at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from
+scratch).
+
+Optional arguments:
+ --db_name
+ is the name of the SQLite file [def: $db_name]
+ --db_dir
+ is the location of the SQLite file [def: $db_dir]
+ --work_dir
+ is the location where temporary files will be downloaded/created [def: $work_dir]
+ --bedtools
+ is the name of the bedtools executable you want to use [def: $bedtools]
+};
+
+GetOptions(
+ "help" => \$help,
+ "db_name=s" => \$db_name,
+ "db_dir=s" => \$db_dir,
+ "work_dir=s" => \$work_dir,
+ "bedtools=s" => \$bedtools,
+ );
+
+my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name";
+my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr;
+
+my ($vol, $path, $file) = File::Spec->splitpath($illumina450k_csv_file);
+
+if (!-e "$work_dir/$file") {
+ download_url($illumina450k_csv_file, $work_dir);
+}
+
+my $array450k_info = parse_450k_file("$work_dir/$file");
+
+my ($vol27k, $path27k, $file27k) = File::Spec->splitpath($illumina27k_bpm_file);
+
+if (!-e "$work_dir/$file27k") {
+ download_url($illumina27k_bpm_file, $work_dir);
+}
+
+my $array27k_info = parse_27k_file("$work_dir/$file27k");
+
+my $array_info = subset_array($array450k_info, $array27k_info);
+
+load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info);
+
+load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold);
+
+exit();
+
+
+sub download_url {
+ my ($url, $work_dir) = @_;
+
+ print "Downloading $url...\n";
+ system("wget -q -N -P $work_dir $url");
+}
+
+
+sub parse_450k_file {
+ my ($illumina450k_csv_file) = @_;
+ my $array;
+
+ open(CSV, $illumina450k_csv_file) or die;
+ my $annotation;
+ my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR");
+ my $cpg_annotations = {
+ 'N_Shelf' => "Shelf_Shore",
+ 'S_Shelf' => "Shelf_Shore",
+ 'N_Shore' => "Shelf_Shore",
+ 'S_Shore' => "Shelf_Shore",
+ 'Island' => "Island"};
+ while () {
+ chomp;
+ my @data = split(",", $_);
+ my $probe_id = $data[0];
+ next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./);
+ my $probe_chr37 = $data[11];
+ my $probe_loc37 = $data[12];
+ my $probe_chr36 = $data[14];
+ my $probe_loc36 = $data[15];
+ my $this_gene_annotation_arrayStr = $data[23];
+ my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA";
+
+ my $this_gene_annotation;
+ if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") {
+ $this_gene_annotation = "IGR";
+ } else {
+ my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr);
+ foreach my $this_a (@this_gene_annotations) {
+ if (grep {$_ eq $this_a} @gene_annotations) {
+ $this_gene_annotation = $this_a;
+ last;
+ }
+ }
+ }
+
+ $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++;
+
+ $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation];
+ }
+ close(CSV);
+# foreach my $this_a (keys %$annotation) { #@gene_annotations) {
+# print $annotation->{$this_a}, "\t", $this_a, "\n";
+# }
+
+ return $array;
+}
+
+
+sub parse_27k_file {
+ my ($illumina27k_bpm_file) = @_;
+ my $array;
+
+ open(CSV, $illumina27k_bpm_file) or die;
+ my $block = "";
+ while () {
+ if (/^\[(\w+)\]/) {
+ $block = $1;
+ }
+ next if ($block ne "Assay");
+
+ chomp;
+ my @data = split(",", $_);
+ my $probe_id = $data[0];
+ my $name = $data[1];
+ my $probe_chr36 = $data[8];
+ my $probe_loc36 = $data[9];
+
+ if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./) {
+# print "Skipping $probe_id\n";
+ next;
+ }
+ if ($probe_id ne $name) {
+ print "ERROR: $probe_id ne $name\n";
+ }
+ $array->{$probe_id} = [$probe_chr36, $probe_loc36];
+ }
+ close(CSV);
+
+ return $array;
+}
+
+sub subset_array {
+ my ($full_array, $sub_array) = @_;
+ my $array;
+ foreach my $probe_id (keys %$full_array) {
+ if ($sub_array->{$probe_id}) {
+ $array->{$probe_id} = $full_array->{$probe_id};
+ print "MISMATCH $probe_id\n" if (($full_array->{$probe_id}->[0] ne $sub_array->{$probe_id}->[0])
+ or
+ ($full_array->{$probe_id}->[1] != $sub_array->{$probe_id}->[1]));
+ }
+ }
+ return $array;
+}
+
+
+sub load_array_1 {
+ my ($dbh, $code_name, $array_info) = @_;
+
+ my $table_name = $code_name;
+ $table_name =~ s/\W//g;
+ $table_name = "array_$table_name";
+ $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)");
+
+ my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)");
+ foreach my $this_probe_id (sort keys $array_info) {
+ my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}};
+ my $location = "$chr:$loc-$loc";
+ $sth->execute($this_probe_id, $location, $gene_group, $cgi_group);
+ }
+ $sth->finish();
+
+ return $table_name;
+}
+
+
+sub load_array {
+ my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_;
+
+ my $sth;
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)");
+ $sth->execute($array_tag, $array_name, $species_name);
+ my $array_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+ if ($array_id == 0) {
+ $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'");
+ }
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)");
+ $sth->execute($species_name, "GRCh37");
+ $sth->execute($species_name, "NCBI36");
+ $sth->finish();
+ my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'");
+ my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'");
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)");
+ $sth->execute($array_id, $human36_assembly_id, "");
+ my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", "");
+ $sth->execute($array_id, $human37_assembly_id, "");
+ my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)");
+ $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", "");
+# my $probe_annotation_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+
+ open(CSV1, ">probe_mapping.csv") or die;
+ open(CSV2, ">probe_annotation.csv") or die;
+# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)");
+# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)");
+ foreach my $this_probe_id (sort keys $array_info) {
+ my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}};
+ print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n";
+ print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n";
+# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n";
+ print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n";
+# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id);
+# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id);
+# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id);
+ }
+ close(CSV1);
+ close(CSV2);
+ system("echo '.mode csv
+.import probe_mapping.csv probe_mapping
+.import probe_annotation.csv probe_annotation' | sqlite3 $db_name");
+# $sth1->finish();
+# $sth2->finish();
+
+}
+
+sub load_proxy_filter {
+ my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_;
+
+ my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0];
+ my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir);
+ my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed";
+ my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file";
+ system($runstr) == 0 or die "Error while running bedtools: $?";
+
+ my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)");
+ $sth->execute($array_id, "Distance-based: 1kb");
+
+ open(BED, $this_output_bed_file) or die;
+ my $all_probes;
+ my $mapping_probes;
+ while () {
+ chomp;
+ my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_);
+ $all_probes->{$probe1} = 1;
+ if ($probe1 ne $probe2) {
+ $mapping_probes->{$probe1}->{$probe2} = 1;
+ }
+ }
+ close(BED);
+ open(CSV, ">proxy_filter.csv") or die;
+ foreach my $probe (sort keys %$all_probes) {
+ if (defined($mapping_probes->{$probe})) {
+ print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n";
+ } else {
+ print CSV "$array_id,$probe,NONE\n";
+ }
+ }
+ close(CSV);
+ system("echo '.mode csv
+.import proxy_filter.csv proxy_filter' | sqlite3 $db_name");
+
+}
+
+sub dump_array_bed_file {
+ my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_;
+ my $sql = "SELECT probe_mapping_id
+ FROM probe_mapping_info
+ JOIN assembly USING (assembly_id)
+ WHERE array_id = $this_array_id
+ AND assembly_name = '$assembly_name'";
+ my $probe_mapping_id = $dbh->selectrow_array($sql);
+ if (!$probe_mapping_id) {
+ die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n";
+ }
+
+ $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id";
+ my $probes = $dbh->selectall_arrayref($sql);
+
+ my $bed_file = "$work_dir/array_${this_array_id}.bed";
+ open(BED, ">$bed_file") or die;
+ foreach my $this_probe (sort _sort_probes @$probes) {
+ print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n";
+ }
+ close(BED);
+
+ return $bed_file;
+}
+
+sub _sort_probes {
+ my $chr_a = $a->[1];
+ my $chr_b = $b->[1];
+ my $loc_a = $a->[2];
+ my $loc_b = $b->[2];
+ $chr_a =~ s/chr//;
+ $chr_b =~ s/chr//;
+ if ($chr_a eq $chr_b) {
+ return $loc_a <=> $loc_b;
+ } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) {
+ return $chr_a <=> $chr_b;
+ } elsif ($chr_a =~ /^\d/) {
+ return -1;
+ } elsif ($chr_b =~ /^\d/) {
+ return 1;
+ } else {
+ return $chr_a cmp $chr_b;
+ }
+}
+
+
+exit();
diff --git a/database/load_450k_array.pl b/database/load_450k_array.pl
new file mode 100644
index 0000000..3dadd80
--- /dev/null
+++ b/database/load_450k_array.pl
@@ -0,0 +1,287 @@
+#! /usr/bin/env perl
+use strict;
+use warnings;
+
+use Getopt::Long;
+use File::Spec qw(splitpath);
+use DBI;
+
+my $db_dir = ".";
+my $db_name = "eforge_1.2.db";
+my $array_tag = "450k";
+my $array_name = "Illumina Human 450k array";
+my $species = "Homo sapiens";
+my $proxy_threshold = 1000;
+my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv';
+my $work_dir = ".";
+my $bedtools = "bedtools";
+
+my $help;
+
+my $desc = qq{load_450k_array.pl [options]
+
+DESCRIPTION:
+
+This script loads the probe locations and annotations of the Illumina Human 450k methylation array
+into the eFORGE database.
+
+Note that you *must* load the arrays before loading the datasets. If you want to include new arrays
+at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from
+scratch).
+
+Optional arguments:
+ --db_name
+ is the name of the SQLite file [def: $db_name]
+ --db_dir
+ is the location of the SQLite file [def: $db_dir]
+ --work_dir
+ is the location where temporary files will be downloaded/created [def: $work_dir]
+ --bedtools
+ is the name of the bedtools executable you want to use [def: $bedtools]
+};
+
+GetOptions(
+ "help" => \$help,
+ "db_name=s" => \$db_name,
+ "db_dir=s" => \$db_dir,
+ "work_dir=s" => \$work_dir,
+ "bedtools=s" => \$bedtools,
+ );
+
+my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name";
+my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr;
+
+my ($vol, $apth, $file) = File::Spec->splitpath($illumina450k_csv_file);
+
+if (!-e "$work_dir/$file") {
+ download_url($illumina450k_csv_file, $work_dir);
+}
+
+my $array_info = parse_450k_file("$work_dir/$file");
+
+load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info);
+
+load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold);
+
+exit();
+
+
+sub download_url {
+ my ($url, $work_dir) = @_;
+
+ print "Downloading $url...\n";
+ system("wget -q -N -P $work_dir $url");
+}
+
+
+sub parse_450k_file {
+ my ($illumina450k_csv_file) = @_;
+ my $array;
+
+ open(CSV, $illumina450k_csv_file) or die;
+ my $annotation;
+ my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR");
+ my $cpg_annotations = {
+ 'N_Shelf' => "Shelf_Shore",
+ 'S_Shelf' => "Shelf_Shore",
+ 'N_Shore' => "Shelf_Shore",
+ 'S_Shore' => "Shelf_Shore",
+ 'Island' => "Island"};
+ while () {
+ chomp;
+ my @data = split(",", $_);
+ my $probe_id = $data[0];
+ next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./);
+ my $probe_chr37 = $data[11];
+ my $probe_loc37 = $data[12];
+ my $probe_chr36 = $data[14];
+ my $probe_loc36 = $data[15];
+ my $this_gene_annotation_arrayStr = $data[23];
+ my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA";
+
+ my $this_gene_annotation;
+ if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") {
+ $this_gene_annotation = "IGR";
+ } else {
+ my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr);
+ foreach my $this_a (@this_gene_annotations) {
+ if (grep {$_ eq $this_a} @gene_annotations) {
+ $this_gene_annotation = $this_a;
+ last;
+ }
+ }
+ }
+
+ $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++;
+
+ $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation];
+ }
+ close(CSV);
+# foreach my $this_a (keys %$annotation) { #@gene_annotations) {
+# print $annotation->{$this_a}, "\t", $this_a, "\n";
+# }
+
+ return $array;
+}
+
+
+sub load_array_1 {
+ my ($dbh, $code_name, $array_info) = @_;
+
+ my $table_name = $code_name;
+ $table_name =~ s/\W//g;
+ $table_name = "array_$table_name";
+ $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)");
+
+ my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)");
+ foreach my $this_probe_id (sort keys $array_info) {
+ my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}};
+ my $location = "$chr:$loc-$loc";
+ $sth->execute($this_probe_id, $location, $gene_group, $cgi_group);
+ }
+ $sth->finish();
+
+ return $table_name;
+}
+
+
+sub load_array {
+ my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_;
+
+ my $sth;
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)");
+ $sth->execute($array_tag, $array_name, $species_name);
+ my $array_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+ if ($array_id == 0) {
+ $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'");
+ }
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)");
+ $sth->execute($species_name, "GRCh37");
+ $sth->execute($species_name, "NCBI36");
+ $sth->finish();
+ my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'");
+ my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'");
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)");
+ $sth->execute($array_id, $human36_assembly_id, "");
+ my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", "");
+ $sth->execute($array_id, $human37_assembly_id, "");
+ my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)");
+ $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", "");
+# my $probe_annotation_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+
+ open(CSV1, ">probe_mapping.csv") or die;
+ open(CSV2, ">probe_annotation.csv") or die;
+# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)");
+# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)");
+ foreach my $this_probe_id (sort keys $array_info) {
+ my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}};
+ print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n";
+ print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n";
+# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n";
+ print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n";
+# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id);
+# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id);
+# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id);
+ }
+ close(CSV1);
+ close(CSV2);
+ system("echo '.mode csv
+.import probe_mapping.csv probe_mapping
+.import probe_annotation.csv probe_annotation' | sqlite3 $db_name");
+# $sth1->finish();
+# $sth2->finish();
+
+}
+
+sub load_proxy_filter {
+ my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_;
+
+ my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0];
+ my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir);
+ my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed";
+ my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file";
+ system($runstr) == 0 or die "Error while running bedtools: $?";
+
+ my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)");
+ $sth->execute($array_id, "Distance-based: 1kb");
+
+ open(BED, $this_output_bed_file) or die;
+ my $all_probes;
+ my $mapping_probes;
+ while () {
+ chomp;
+ my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_);
+ $all_probes->{$probe1} = 1;
+ if ($probe1 ne $probe2) {
+ $mapping_probes->{$probe1}->{$probe2} = 1;
+ }
+ }
+ close(BED);
+ open(CSV, ">proxy_filter.csv") or die;
+ foreach my $probe (sort keys %$all_probes) {
+ if (defined($mapping_probes->{$probe})) {
+ print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n";
+ } else {
+ print CSV "$array_id,$probe,NONE\n";
+ }
+ }
+ close(CSV);
+ system("echo '.mode csv
+.import proxy_filter.csv proxy_filter' | sqlite3 $db_name");
+
+}
+
+sub dump_array_bed_file {
+ my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_;
+ my $sql = "SELECT probe_mapping_id
+ FROM probe_mapping_info
+ JOIN assembly USING (assembly_id)
+ WHERE array_id = $this_array_id
+ AND assembly_name = '$assembly_name'";
+ my $probe_mapping_id = $dbh->selectrow_array($sql);
+ if (!$probe_mapping_id) {
+ die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n";
+ }
+
+ $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id";
+ my $probes = $dbh->selectall_arrayref($sql);
+
+ my $bed_file = "$work_dir/array_${this_array_id}.bed";
+ open(BED, ">$bed_file") or die;
+ foreach my $this_probe (sort _sort_probes @$probes) {
+ print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n";
+ }
+ close(BED);
+
+ return $bed_file;
+}
+
+sub _sort_probes {
+ my $chr_a = $a->[1];
+ my $chr_b = $b->[1];
+ my $loc_a = $a->[2];
+ my $loc_b = $b->[2];
+ $chr_a =~ s/chr//;
+ $chr_b =~ s/chr//;
+ if ($chr_a eq $chr_b) {
+ return $loc_a <=> $loc_b;
+ } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) {
+ return $chr_a <=> $chr_b;
+ } elsif ($chr_a =~ /^\d/) {
+ return -1;
+ } elsif ($chr_b =~ /^\d/) {
+ return 1;
+ } else {
+ return $chr_a cmp $chr_b;
+ }
+}
+
+
+exit();
diff --git a/database/load_dataset.pl b/database/load_dataset.pl
new file mode 100644
index 0000000..6c947d3
--- /dev/null
+++ b/database/load_dataset.pl
@@ -0,0 +1,416 @@
+#! /usr/bin/env perl
+use strict;
+use warnings;
+
+use Getopt::Long;
+use DBI;
+
+my $db_dir = ".";
+my $db_name = "eforge_1.1.db";
+my $dataset_name = "ENCODE";
+my $dataset_tag = "encode";
+my $decode_file = "encode.decode";
+my $work_dir = "/tmp";
+my $species_name = "Homo sapiens";
+my $assembly_name = "GRCh37";
+my $bedtools = "bedtools";
+
+my $help;
+
+my $desc = qq{load_dataset.pl [options]
+
+DESCRIPTION:
+
+This script reads a 'decode' file which contains references to a list of samples, each of them
+corresponding to a given dataset. Each of these files is a BED or BED-like file that is read by
+bedtools to find overlaps with each and every array loaded in the eFORGE database.
+
+Note that you *must* load the arrays first. If you want to include new arrays at a later date, you
+will have to reload all the datasets again (i.e. you will have to re-start from scratch).
+
+Required parameters:
+ --tag or --dataset_tag
+ the ID for this database. This needs to be unique.
+ --name or --dataset_name
+ the name for this database. This can be a longer description. It will be used in the web interface.
+ --decode_file
+ the file with the information about each sample in this dataset
+
+Optional parameters:
+ --db_name
+ is the name of the SQLite file [def: $db_name]
+ --db_dir
+ is the location of the SQLite file [def: $db_dir]
+ --work_dir
+ is the location where temporary files will be downloaded/created [def: $work_dir]
+ --bedtools
+ is the name of the bedtools executable you want to use [def: $bedtools]
+ --species
+ is the name of the species [def: $species_name]
+ --assembly
+ is the name of the assembly [def: $assembly_name]
+};
+
+GetOptions(
+ "help" => \$help,
+ "db_name=s" => \$db_name,
+ "db_dir=s" => \$db_dir,
+ "tag|dataset_tag=s" => \$dataset_tag,
+ "name|dataset_name=s" => \$dataset_name,
+ "decode_file=s" => \$decode_file,
+ "work_dir=s" => \$work_dir,
+ "species=s" => \$species_name,
+ "assembly=s" => \$assembly_name,
+ );
+
+if ($help) {
+ print $desc;
+ exit(0);
+}
+
+my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name";
+my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr;
+
+system("mkdir -p $work_dir");
+
+my $decode_table = get_decode_table($decode_file);
+
+my $dataset_id = load_dataset($dbh, $species_name, $decode_table, $dataset_name, $dataset_tag);
+
+download_bed_files($decode_table, $work_dir);
+
+my $arrays = get_all_arrays_for_species($dbh, $species_name);
+
+foreach my $this_array (@$arrays) {
+ my ($this_array_id, $this_array_name) = @$this_array;
+ my $sorted_array_bed_file = dump_array_bed_file($dbh, $this_array_id, $assembly_name, $work_dir);
+ my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $this_array_id, $this_array_name);
+ my $concatenated_overlaps_bed_file = paste_files($single_overlaps_bed_files, $work_dir, $this_array_id);
+ my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir, $this_array_id);
+ load_bitstrings($dbh, $db_name, $final_overlaps_bed_file, $this_array_id, $dataset_id);
+}
+
+#
+
+
+exit();
+
+my $input_bed_files = get_input_bed_files_from_decode_table($decode_file);
+
+exit(0);
+
+sub load_dataset {
+ my ($dbh, $species_name, $decode_table, $dataset_name) = @_;
+ my $dataset_id;
+
+ my $sth;
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO dataset (dataset_tag, dataset_name, species_name) VALUES (?, ?, ?)");
+ $sth->execute($dataset_tag, $dataset_name, $species_name);
+ $dataset_id = $dbh->last_insert_id("", "", "", "");
+ $sth->finish();
+ if ($dataset_id == 0) {
+ $dataset_id = $dbh->selectrow_array("SELECT dataset_id FROM dataset WHERE dataset_name = '$dataset_name' AND species_name = '$species_name'");
+ }
+
+
+ $sth = $dbh->prepare("INSERT OR IGNORE INTO sample (dataset_id, sample_order, file, lab, datatype, cell, tissue, shortcell, individual, acc, url)
+ VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)");
+ my $sample_order = 1;
+ foreach my $this_sample (@$decode_table) {
+ $sth->execute($dataset_id,
+ $sample_order,
+ $this_sample->{file},
+ $this_sample->{lab},
+ $this_sample->{datatype},
+ $this_sample->{cell},
+ $this_sample->{tissue},
+ $this_sample->{shortcell},
+ $this_sample->{individual},
+ $this_sample->{acc},
+ $this_sample->{url});
+ $sample_order++;
+ }
+
+ return($dataset_id);
+}
+
+sub load_bitstrings {
+ my ($dbh, $db_name, $bed_file, $array_id, $dataset_id) = @_;
+
+# my $sql = "INSERT INTO probe_bitstring (array_id, probe_id, dataset_id, sum, bit)
+# VALUES (?, ?, ?, ?, ?)";
+# my $sth = $dbh->prepare($sql);
+ open(BED, $bed_file) or die "Cannot open BED file <$bed_file>\n";
+ open(CSV, ">probe_bitstring.csv") or die "Cannot open CVS temporary file \n";
+ while() {
+ chomp;
+ my ($chr, $start, $end, $probe_id, $sum, $bitstring) = split("\t", $_);
+ print CSV join(",", $array_id, $probe_id, $dataset_id, $sum, $bitstring), "\n";
+# $sth->execute($array_id, $probe_id, $dataset_id, $sum, $bitstring);
+ }
+ close(BED);
+ close(CSV);
+ system("echo '.mode csv
+.import probe_bitstring.csv probe_bitstring' | sqlite3 $db_name");
+# $sth->finish();
+}
+
+=head2 add_sum_column_to_concatenated_bedfile
+
+ Arg[1] : string $concatenated_overlaps_bed_file (location of the input BED file with 0/1 flags on the 4th column)
+ Arg[2] : string $work_dir (where to put the temporary files)
+ Example : my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir);
+ Description : Reads the input BED file ($concatenated_overlaps_bed_file) which contains a series
+ of 0 and 1 flags in the 4th column. This function reads the number of ones in that
+ column and include that value in the output BED file. The output BED file will
+ contain that number in the 4th column and the series of flag in the 5th colum.
+ Returns : string $final_overlaps_bed_file (the location of the resulting BED file)
+ Exceptions : Dies if error when opening the files
+
+=cut
+
+sub add_sum_column_to_concatenated_bedfile {
+ my ($concatenated_overlaps_bed_file, $work_dir, $array_id) = @_;
+ my $final_overlaps_bed_file = "$work_dir/final_overlaps.array_${array_id}.bed";
+
+ open(BED_IN, $concatenated_overlaps_bed_file) or die "Cannot open BED file <$concatenated_overlaps_bed_file>\n";
+ open(BED_OUT, ">$final_overlaps_bed_file") or die "Cannot open BED file <$final_overlaps_bed_file>\n";
+ while() {
+ chomp;
+ my ($this_chr, $this_start, $this_end, $this_probe, $this_bitstring) = split("\t", $_);
+ my $num = $this_bitstring =~ tr/1/1/;
+ print BED_OUT join("\t", $this_chr, $this_start, $this_end, $this_probe, $num, $this_bitstring), "\n";
+ }
+ close(BED_IN);
+ close(BED_OUT);
+
+ return $final_overlaps_bed_file;
+}
+
+
+=head2 run_single_overlap_bedtools
+
+ Arg[1] : string $bedtools (either full path or just the binary if in the $PATH)
+ Arg[2] : string $work_dir (where to put the temporary files)
+ Arg[3] : string $sorted_450k_bed_file (location of the BED file with sorted 450K features)
+ Arg[4] : arrayref of hash $decode_table
+ Example : my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_450k_bed_file, $decode_table);
+ Description : Run bedtools on the sorted 450K features vs all the BED DNAse features, one at a time.
+ Returns : arrayref of string $total_overlaps_bed_files (the locations of the resulting BED files)
+ Exceptions : Dies if error when running bedtools
+
+=cut
+
+sub run_single_overlap_bedtools {
+ my ($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $array_id, $array_name) = @_;
+ my $single_overlap_bed_files = [];
+
+ foreach my $this_input_bed_file (map {$_->{"file"}} @$decode_table) {
+ print "Overlap between $array_name and $this_input_bed_file...\n";
+ my $this_output_bed_file = $this_input_bed_file;
+ $this_output_bed_file =~ s/.+\///;
+ $this_output_bed_file = "$work_dir/single_overlaps.array_${array_id}.$this_output_bed_file";
+ my $runstr = "$bedtools intersect -c -a $sorted_array_bed_file -b $work_dir/$this_input_bed_file > $this_output_bed_file";
+ system($runstr) == 0 or die "Error while running bedtools: $?";
+ push(@$single_overlap_bed_files, $this_output_bed_file);
+ }
+
+ return $single_overlap_bed_files;
+}
+
+
+sub get_decode_table {
+ my ($decode_file) = @_;
+ my $decode_table;
+
+ open(DECODE, $decode_file) or die "Cannot open decode file <$decode_file>\n";
+ my $whole_text = join("\n", );
+ $whole_text =~ s/[\r\n]+/\n/g;
+ my @lines = split("\n", $whole_text);
+ close(DECODE);
+
+ my @header = split("\t", shift(@lines));
+
+ foreach my $this_line (@lines) {
+ my @data = split("\t", $this_line);
+ my $decode_record = {};
+ for (my $i=0; $i<@header; $i++) {
+ $decode_record->{$header[$i]} = $data[$i];
+ }
+ # Check that file and URL match
+ die "File: ".$decode_record->{"file"}."\nURL: ".$decode_record->{"url"}."\nOn line: $this_line"
+ if ($decode_record->{"url"} !~ $decode_record->{"file"});
+ $decode_record->{"file"} = $decode_record->{"url"};
+ $decode_record->{"file"} =~ s/.+\///g;
+ push(@$decode_table, $decode_record);
+ }
+
+ return $decode_table;
+}
+
+sub download_bed_files {
+ my ($decode_table, $work_dir) = @_;
+
+ foreach my $this_decode_entry (@$decode_table) {
+ my $url = $this_decode_entry->{"url"};
+ my $file = $this_decode_entry->{"file"};
+ if (!-e "$work_dir/$file") {
+ download_url($url, $work_dir);
+ }
+ }
+}
+
+
+sub download_url {
+ my ($url, $work_dir) = @_;
+
+ print "Downloading $url...\n";
+ system("wget", "-q", "-N", "-P", $work_dir, $url) == 0
+ or die "Error: wget -q -N -P $work_dir $url\n$!";
+}
+
+
+sub paste_files {
+ my ($files, $work_dir, $array_id) = @_;
+ my $output_file = "$work_dir/concat_overlaps.array_${array_id}.bed";
+
+ my $max_num_files = 200;
+ my $c = 0;
+ my $temp_output_file;
+ my @original_files = @$files;
+ while (@$files > 1) {
+ $c++;
+ $temp_output_file = "$work_dir/temp.$$.$c.paste_files.txt";
+ my $input_files = [splice(@$files, 0, $max_num_files)];
+# print STDERR "Merging ", join(", ", @$input_files), " into $temp_output_file\n";
+ merge_files($temp_output_file, $input_files);
+ unshift(@$files, $temp_output_file);
+ }
+ rename($temp_output_file, $output_file);
+
+ unlink glob "$work_dir/temp.$$.*.paste_files.txt";
+
+#
+#
+#
+#
+# unlink @original_files;
+#
+#
+#
+#
+
+ return $output_file;
+}
+
+
+sub merge_files {
+ my ($output_file, $input_files) = @_;
+ my @fhs;
+ my $c = 0;
+
+ foreach my $this_input_file (@$input_files) {
+ open($fhs[$c++], $this_input_file) or die "Cannot open $this_input_file: $!\n";
+ }
+ open(OUT, ">$output_file") or die "Cannot open $output_file: $!\n";
+
+ my $first_fh = shift(@fhs);
+
+ while (1) {
+ my $line = <$first_fh>;
+ chomp($line);
+ my ($chr, $start, $end, $probe_id, $value) = split("\t", $line);
+ print OUT join("\t", $chr, $start, $end, $probe_id, $value);
+ foreach my $this_fh (@fhs) {
+ my $line = <$this_fh>;
+ chomp($line);
+ my ($this_chr, $this_start, $this_end, $this_probe_id, $this_value) = split("\t", $line);
+ if (($this_chr ne $chr) or ($this_start != $start) or ($this_end != $end) or ($this_probe_id ne $probe_id)) {
+ die "Files do not contain the same $chr-$start-$end-$probe_id lines\n";
+ }
+ print OUT $this_value;
+ }
+ print OUT "\n";
+ if (eof($first_fh)) {
+ last;
+ }
+ }
+
+ foreach my $this_fh (@fhs) {
+ close($this_fh);
+ }
+ close(OUT);
+}
+
+sub get_all_arrays_for_species {
+ my ($dbh, $species) = @_;
+ my $arrays;
+
+ my $sth = $dbh->prepare("SELECT array_id, array_name FROM array WHERE species_name = ?");
+ $sth->execute($species);
+ $arrays = $sth->fetchall_arrayref();
+ $sth->finish();
+
+ return $arrays;
+}
+
+sub get_probe_mapping_id {
+ my ($dbh, $this_array_id, $assembly_name) = @_;
+ my $sql = "SELECT probe_mapping_id
+ FROM probe_mapping_info
+ JOIN assembly USING (assembly_id)
+ WHERE array_id = $this_array_id
+ AND assembly_name = '$assembly_name'";
+ my $probe_mapping_id = $dbh->selectrow_array($sql);
+ return($probe_mapping_id);
+}
+
+sub dump_array_bed_file {
+ my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_;
+ my $sql = "SELECT probe_mapping_id
+ FROM probe_mapping_info
+ JOIN assembly USING (assembly_id)
+ WHERE array_id = $this_array_id
+ AND assembly_name = '$assembly_name'";
+ my $probe_mapping_id = $dbh->selectrow_array($sql);
+
+ $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id";
+ my $probes = $dbh->selectall_arrayref($sql);
+
+ my $bed_file = "$work_dir/array_${this_array_id}.bed";
+ open(BED, ">$bed_file") or die "Cannot open temporary BED file <$bed_file>\n";
+ foreach my $this_probe (sort _sort_probes @$probes) {
+ print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n";
+ }
+ close(BED);
+
+ return $bed_file;
+}
+
+sub _sort_probes {
+ my $chr_a = $a->[1];
+ my $chr_b = $b->[1];
+ my $loc_a = $a->[2];
+ my $loc_b = $b->[2];
+ $chr_a =~ s/chr//;
+ $chr_b =~ s/chr//;
+ if ($chr_a eq $chr_b) {
+ return $loc_a <=> $loc_b;
+ } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) {
+ return $chr_a <=> $chr_b;
+ } elsif ($chr_a =~ /^\d/) {
+ return -1;
+ } elsif ($chr_b =~ /^\d/) {
+ return 1;
+ } else {
+ return $chr_a cmp $chr_b;
+ }
+}
+
+exit();
+
+
+
+
+
+
diff --git a/eForge/eForge.pm b/eForge/eForge.pm
index 824262d..7121134 100644
--- a/eForge/eForge.pm
+++ b/eForge/eForge.pm
@@ -1,26 +1,55 @@
package eForge::eForge;
-use 5.010;
-use strict;
-use warnings FATAL => 'all';
-use Storable;
-
=head1 NAME
-eForge - The great new eForge!
+eForge::eForge - Interface with the DB and various other common functions for eForge
=head1 VERSION
Version 0.01
+=head1 LICENCE AND COPYRIGHT
+
+Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; version 2 dated June, 1991 or at your option
+any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+A copy of the GNU General Public License is available in the source tree;
+if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+=head1 CONTACT
+
+Charles Breeze, C<< >>
+
+Javier Herrero, C<< >>
+
+=head1 ACKNOWLEDGEMENTS
+
+This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI
+
=cut
+use 5.010;
+use strict;
+use warnings FATAL => 'all';
+use Storable;
+
+
my $MAX_SQL_VARIABLES = 999;
our $VERSION = '0.01';
our (@ISA, @EXPORT);
use Exporter;
@ISA = qw(Exporter);
-@EXPORT = qw(process_file match process_bits get_bits fetch_rsid fetch_loc get_cells assign bkgrdstat prox_filter);
+@EXPORT = qw(get_all_datasets get_all_arrays get_all_proxy_filters process_file match process_bits get_bits get_cells assign bkgrdstat prox_filter);
=head1 SYNOPSIS
@@ -28,12 +57,13 @@ Provide functional modules for eForge
=head1 EXPORT
+get_all_datasets
+get_all_arrays
+get_all_proxy_filters
process_file
match
process_bits
get_bits
-fetch_rsid
-fetch_loc
get_cells
assign
bkgrdstat
@@ -67,85 +97,66 @@ sub bkgrdstat{
say $bfh join("\t", $flag, "cpg_island_relationship", @cpg_island_relationship);
}
+
=head2 process_file
-Processes various file formats.
+ Arg[1] : FILEHANDLE $input_fh
+ Arg[2] : string $format
+ Arg[3] : DB-connection-handle $dbh
+ Arg[4] : string $bkgd
+ Arg[5] : numeric $filter
+ Returns : arrayref of $probe_ids (string)
+ Example : my $probe_ids = process_file($fh, "probeid", $dbh, '450k', undef);
+ Description : Reads the list of probe IDs or locations from the file. If the file contains
+ locations, these will be translated into probe_ids
+ Exceptions :
=cut
sub process_file {
- my ($fh, $format, $sth, $filter) = @_;
- my @snps;
- if ($format =~ /probeid/){
- while (<$fh>){
+ my ($fh, $format, $dbh, $bkgd, $filter) = @_;
+ my $probe_ids = [];
+
+ if ($format =~ /^probe/i) {
+ while (<$fh>) {
next if /^#/;
chomp;
- my $rs;
+ my $probe_id;
if (defined $filter) {
my $pval;
- ($rs, $pval) = split /\s+/, $_;
+ ($probe_id, $pval) = split /\s+/, $_;
next unless $pval >= $filter;
- }
- else{
- ($rs, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-)
- }
- my @rsid = split /\:/, $rs;
- my $rsid = pop @rsid; # take the last one for want of a better idea.
- push @snps, $rsid;
- }
- }
- elsif ($format =~ /ian/){
- while (<$fh>){
- my ($chr, $beg, $end, $rsid, $p, $pval) = split "\t", $_;
- if (defined $filter) {
- next unless $pval >= $filter;
- }
- my @rsid = split /\:/, $rsid; # to deal with multiple rsids
- $rsid = pop @rsid; # take the last one for want of a better idea. Can't take all as they are the same thing.
- push @snps, $rsid;
- }
- }
- elsif ($format =~ /vcf/){
- while (<$fh>){
- next if /^#/;
- my ($chr, $beg, $rsid) = split "\t", $_;
+ } else {
+ ($probe_id, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-)
+ }
+ push @$probe_ids, $probe_id;
+ }
+
+ } elsif ($format =~ /^bed/i) {
+ my $locations = [];
+ while (<$fh>) {
+ next if /^track/;
+ chomp;
+ my ($chr, $from, $to) = split "\t", $_;
+ next if (!defined($to));
unless ($chr =~ /^chr/){
$chr = "chr". $chr;
- }
- if ($rsid =~ /^cg\d+/){
- push @snps, $rsid;
- }
- else {
- my $loc = "$chr:$beg-$beg";
- #get the rsid from the db
- $rsid = fetch_rsid($loc, $sth);
- push @snps, $rsid if defined $rsid;
- }
- }
- }
- elsif ($format =~ /bed|tabix/){
- while (<$fh>){
- my $loc;
- if ($format =~/bed/){
- next if /^track/;
- chomp;
- my ($chr, $beg, $end) = split "\t", $_;
- unless ($chr =~ /^chr/){
- $chr = "chr". $chr;
- }
- $loc = "$chr:$beg-$beg";
- }
- elsif ($format =~ /tabix/){
- chomp;
- $loc = $_;
- }
- #get the $rsid from the db
- my $rsid = fetch_rsid($loc, $sth);
- push @snps, $rsid if defined $rsid;
- }
- }
- return @snps;
- }
+ }
+ push(@$locations, [$chr, $from]);
+ }
+ $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations);
+
+ } elsif ($format =~ /^tabix/i) {
+ my $locations = [];
+ while (<$fh>) {
+ chomp;
+ my ($chr, $from, $to) = $_ =~ /(.+)\:(\d+)\-(\d+)/;
+ push(@$locations, [$chr, $from]);
+ }
+ $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations);
+ }
+ return $probe_ids;
+}
=head2 match
@@ -240,51 +251,154 @@ sub match{
=head2 process_bits
-Processes bitstrings to get a count of overlaps for each cell type.
+ Arg[1] : arrayref of arrays $rows ($probe_id, $sum, $bit_string, $feature, $CGI_context)
+ Arg[2] : arrayref of strings $cells (shortname for the cells in the dataset)
+ Arg[3] : string $dataset
+ Returns : hashref $stats
+ Example : my $result = process_bits($rows, $cells, 'erc');
+ Description : Returns a reference to a complex hash with stats from the rows. These are split
+ into 'MVPS' and 'CELLS'. The former contains 'SUM' and 'PARAMS' for each probe ID
+ while the latter contains 'COUNT' and 'MVPS' for each cell.
+ Exceptions : Dies if the number of cells does not match the length of the bit string.
=cut
-sub process_bits{
+sub process_bits {
my ($rows, $cells, $data) = @_;
my %test;
my @test_cells;
my @indexes = 0..(@$cells-1);
foreach my $row (@{$rows}){
- my ($location, $probeid, $sum, $bit_string, $feature, $cpg_island_relationship);
- if ($data eq "erc"){
- ($location, $probeid, undef, undef, $bit_string, $sum, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row;
- }
- elsif ($data eq "encode"){
- ($location, $probeid, $bit_string, $sum, undef, undef, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row;
- }
- elsif ($data eq "blueprint"){
- ($location, $probeid, undef, undef, undef, undef, $bit_string, $sum, undef, undef, $feature, $cpg_island_relationship) = @$row;
- }
- elsif ($data eq "erc2"){
- ($location, $probeid, undef, undef, undef, undef, undef, undef, $bit_string, $sum, $feature, $cpg_island_relationship) = @$row;
- }
+ my ($probeid, $sum, $bit_string, $feature, $cpg_island_relationship) = @$row;
$test{'MVPS'}{$probeid}{'SUM'} = $sum;
$test{'MVPS'}{$probeid}{'PARAMS'} = join("\t", $feature, $cpg_island_relationship);
- die if (scalar(@$cells) ne length($bit_string));
+ die "For $data, found ".scalar(@$cells)." cells for ".length($bit_string)." bits\n" if (scalar(@$cells) ne length($bit_string));
foreach my $index (@indexes) {
## $bit_string is a string made of 0s and 1s. If it is a 1 for this position, count and push
if (substr($bit_string, $index, 1)) {
$test_cells[$index][0]++;
push @{$test_cells[$index][1]}, $probeid;
}
- }
- }
+ }
+ }
my $index = 0;
foreach my $cell (@$cells){
$test{'CELLS'}{$cell}{'COUNT'} = $test_cells[$index][0] if ($test_cells[$index][0]);
$test{'CELLS'}{$cell}{'MVPS'} = $test_cells[$index][1] if ($test_cells[$index][1]);
$index++;
- }
+ }
return \%test;
- }
+}
+
+
+=head2 get_all_datasets
+
+ Arg[1] : DB-handle $dbh
+ Arg[2] : (optional) string $species_name
+ Returns : arrayref of hashes (tag/name)
+ Example : my $all_datasets = get_all_dataset($dbh);
+ Description : Returns the list of all datasets in the DB. It returns an arrayref of hashes. Each
+ hash has two keys: 'tag' (string ID of the dataset) and 'name' (full name). You
+ can limit the dataset to the ones available for a given species.
+ Exceptions :
+
+=cut
+
+sub get_all_datasets {
+ my ($dbh, $species_name) = @_;
+ my $datasets;
+
+ my $sql = "SELECT dataset_tag, dataset_name FROM dataset ORDER BY dataset_id";
+ my @bind_params = ();
+ if ($species_name) {
+ $sql .= " WHERE species_name = ?";
+ push(@bind_params, $species_name);
+ }
+ my ($tag, $name);
+ my $sth = $dbh->prepare($sql);
+ $sth->execute(@bind_params);
+ $sth->bind_columns(\$tag, \$name);
+ while ($sth->fetch) {
+ push(@$datasets, {tag => $tag, name => $name});
+ }
+
+ return($datasets);
+}
+=head2 get_all_arrays
+
+ Arg[1] : DB-handle $dbh
+ Arg[2] : (optional) string $species_name
+ Returns : arrayref of hashes (tag/name)
+ Example : my $all_arrays = get_all_arrays($dbh);
+ Description : Returns the list of all arrays in the DB. It returns an arrayref of hashes. Each
+ hash has two keys: 'tag' (string ID of the array) and 'name' (full name). You
+ can limit the arrays to the ones available for a given species.
+ Exceptions :
+
+=cut
+
+sub get_all_arrays {
+ my ($dbh, $species_name) = @_;
+ my $arrays;
+
+ my $sql = "SELECT array_tag, array_name FROM array order by array_id";
+ my @bind_params = ();
+ if ($species_name) {
+ $sql .= " WHERE species_name = ?";
+ push(@bind_params, $species_name);
+ }
+ my ($tag, $name);
+ my $sth = $dbh->prepare($sql);
+ $sth->execute();
+ $sth->bind_columns(\$tag, \$name);
+ while ($sth->fetch) {
+ push(@$arrays, {tag => $tag, name => $name});
+ }
+
+ return($arrays);
+}
+
+
+=head2 get_all_proxy_filters
+
+ Arg[1] : DB-handle $dbh
+ Arg[2] : (optional) string $bkgd
+ Returns : hashref of proxy-filters (string)
+ Example : my $proxy_filters = get_all_proxy_filters($dbh, '450k');
+ Description : Returns the list of proxy filters available in the DB. It returns a hashref whose
+ keys are the bkgd names (i.e. array tags) and values are the name of the proxy
+ filter. At the moment the schema supports just one proxy filter per array.
+ If you provide a $bkgd, the result will be limited to that array. Note that you
+ will still get a hashref with exactly the same structure. Only the content will
+ be limited.
+ Exceptions :
+
+=cut
+
+sub get_all_proxy_filters {
+ my ($dbh, $array_tag) = @_;
+ my $proxy_filters;
+
+ my $sql = "SELECT array_tag, description FROM proxy_filter_info JOIN array USING (array_id)";
+ my @bind_params = ();
+ if ($array_tag) {
+ $sql .= " WHERE array_tag = ?";
+ push(@bind_params, $array_tag);
+ }
+ my ($this_array_tag, $description);
+ my $sth = $dbh->prepare($sql);
+ $sth->execute();
+ $sth->bind_columns(\$this_array_tag, \$description);
+ while ($sth->fetch) {
+ $proxy_filters->{$this_array_tag} = $description;
+ }
+
+ return($proxy_filters);
+}
+
=head2 get_bits
Get the bitstrings for an array of mvps from the sqlite db
@@ -292,8 +406,7 @@ Get the bitstrings for an array of mvps from the sqlite db
=cut
sub get_bits{
-
- my ($mvps, $dbh) = @_;
+ my ($dbh, $dataset_tag, $array_tag, $mvps) = @_;
my @results;
for (my $loop = 0; $loop * $MAX_SQL_VARIABLES < @$mvps; $loop++) {
@@ -301,42 +414,60 @@ sub get_bits{
my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1;
$end = @$mvps -1 if ($end >= @$mvps);
- my $sql = "SELECT * FROM bits WHERE probeid IN (?". (",?" x ($end - $start)).")";
+ my $sql = "SELECT probe_id, sum, bit, gene_group, cgi_group
+ FROM probe_annotation
+ JOIN probe_bitstring USING (array_id, probe_id)
+ JOIN dataset USING (dataset_id)
+ JOIN array ON (array.array_id = probe_annotation.array_id)
+ WHERE array_tag = ? and dataset_tag = ?
+ AND probe_id IN (?". (",?" x ($end - $start)).")";
my $sth = $dbh->prepare_cached($sql); #get the blocks form the ld table
- $sth->execute(@$mvps[$start..$end]);
+ $sth->execute($array_tag, $dataset_tag, @$mvps[$start..$end]);
while (my $row = $sth->fetchrow_arrayref()) {
- push @results, [@$row];
+ push @results, [@$row];
}
$sth->finish();
- }
+ }
return \@results;# return the bitstring line from the database
- }
+}
+
-=head2 fetch_rsid
+=head2 fetch_all_probe_ids
-gets the rsid for a SNP where a location is given.
+ Arg[1] : DB-handle $dbh
+ Arg[2] : string $bkgd
+ Arg[3] : arrayref of locations [$chr, $pos]
+ Returns : arrayref of probe IDs (string)
+ Description : Given a list of chromosome names and location pairs, the method fetches the name
+ of the probe ID for that location. To do this successfully, this method requires
+ to know the background (i.e. array) you want to translate the locations to.
+ Exceptions :
=cut
-sub fetch_rsid{
+sub fetch_all_probe_ids {
#gets the rsid for a SNP where a location is given
- my ($loc, $sth) = @_;
- $sth->execute($loc);
- my $result = $sth->fetchall_arrayref();
- my $rsid;
- foreach my $row (@{$result}){
- $rsid = $$row[0];
- }
+ my ($dbh, $bkgd, $locations) = @_;
+
+ my $sth = $dbh->prepare("SELECT probe_id
+ FROM probe_mapping
+ WHERE chr_name = ? AND position = ?");
+ my $probe_ids = [];
+
+ foreach my $this_loc (@$locations) {
+ my ($chr, $pos) = @$this_loc;
+ $sth->execute($chr, $pos);
+ my $result = $sth->fetchall_arrayref();
+ my $probe_id;
+ foreach my $row (@{$result}) {
+ push(@$probe_ids, $$row[0]);
+ }
+ }
$sth->finish();
- if (defined $rsid &&$rsid =~ /^cg\d+/){
- return $rsid;
- }
- else{
- return "no PROBEID match for $loc";
- }
- }
+ return $probe_ids;
+}
=head2 prox_filter
@@ -357,7 +488,7 @@ sub prox_filter{
my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1;
$end = @$mvps -1 if ($end >= @$mvps);
- my $sql = "SELECT probeid,proxy_probes FROM proxy_filter WHERE probeid IN (?". (",?" x ($end - $start)).")";
+ my $sql = "SELECT probe_id,proxy_probes FROM proxy_filter WHERE probe_id IN (?". (",?" x ($end - $start)).")";
my $sth = $dbh->prepare($sql); #get the blocks form the ld table
$sth->execute(@$mvps[$start..$end]);
my $result = $sth->fetchall_arrayref();
@@ -379,118 +510,33 @@ sub prox_filter{
return (\%prox_excluded, @mvps_filtered);
}
-
=head2 get_cells
Read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells.
=cut
-sub get_cells{
- # read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells.
- my ($data, $dbh) = @_;
-
- my $table = "cells_".$data;
-
- # Check that the table exists in the DB (note, some magic here that might be SQLite-specific)
- my @tables = grep {/^cells_/} map {$_ =~ s/"//g; $_ =~ s/^main\.//; $_} $dbh->tables();
- if (!grep {/$table/} @tables) {
- die "The database does not contain information for the data background provided.\n";
+sub get_cells {
+ my ($dataset_tag, $dbh) = @_;
+ my $samples;
+
+ my $sth = $dbh->prepare("SELECT shortcell, tissue, datatype, file, acc FROM dataset JOIN sample USING (dataset_id) WHERE dataset_tag = ? ORDER BY sample_order");
+ $sth->execute($dataset_tag);
+ my ($shortcell, $tissue, $datatype, $file, $acc);
+ $sth->bind_columns(\$shortcell, \$tissue, \$datatype, \$file, \$acc);
+ my ($cells, $tissues);
+ while ($sth->fetch) {
+ $shortcell = "$shortcell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38).
+ push @$cells, $shortcell;
+ $$tissues{$shortcell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order
+ $$tissues{$shortcell}{'datatype'} = $datatype;
+ $$tissues{$shortcell}{'file'} = $file;
+ $$tissues{$shortcell}{'acc'} = $acc;
}
+# use Data::Dumper;
+# print Dumper %$tissues;
- my $sth = $dbh->prepare("SELECT shortcell,tissue,file,acc FROM $table");
- $sth->execute();
- my $ver = $sth->fetchall_arrayref();
- $sth->finish();
- my ($cells, $tissues, $acc);
- foreach my $row (@$ver){
- my $cell = shift @$row;
- my $tissue = shift @$row;
- my $file = shift @$row;
- my $acc = shift @$row;
- $cell = "$cell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38).
- push @$cells, $cell;
- $$tissues{$cell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order
- $$tissues{$cell}{'file'} = $file;
- $$tissues{$cell}{'acc'} = $acc;
- }
- #print Dumper %$tissues;
return ($cells, $tissues); # return
- }
-
-=head2 assign
-
-Assign any maf, gc, tss values to the percentile bins
-
-=cut
-
-#sub assign{
-# #sub routine to assign any maf, gc, tss values to the percentile bins
-# my ($gc, $tss, $maf, $params) = @_;
-# my ($i, $j, $k);
-# my $n = 1;
-# foreach my $pc (@{$$params{'gc'}}){
-# if ($gc <= $pc) {
-# $i = $n;
-# }
-# else{
-# $n++;
-# }
-# }
-# $n=1;
-# foreach my $pc (@{$$params{'tss'}}){
-# if ($tss <= $pc) {
-# $j = $n;
-# }
-# else{
-# $n++;
-# }
-# }
-# $n=1;
-# foreach my $pc (@{$$params{'maf'}}){
-# if ($maf <= $pc) {
-# $k = $n;
-# }
-# else{
-# $n++;
-# }
-# }
-# return ($i, $j, $k);
-# }
-
-=head1 AUTHOR
-
-Charles Breeze, C<< >>
-
-=head1 SUPPORT
-
-You can find documentation for this module with the perldoc command.
-
- perldoc eForge
-
-
-=head1 ACKNOWLEDGEMENTS
-
-
-=head1 LICENSE AND COPYRIGHT
-
-Copyright 2015 Charles Breeze.
-
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; version 2 dated June, 1991 or at your option
-any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-A copy of the GNU General Public License is available in the source tree;
-if not, write to the Free Software Foundation, Inc.,
-51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-
-
-=cut
+}
1;
diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm
index b95aa1f..602ff65 100644
--- a/eForge/ePlot.pm
+++ b/eForge/ePlot.pm
@@ -1,10 +1,5 @@
package eForge::ePlot;
-use 5.010;
-use strict;
-use warnings FATAL => 'all';
-use Sort::Naturally;
-
=head1 NAME
eForge::ePlot - Plotting utilities for eForge
@@ -13,8 +8,41 @@ eForge::ePlot - Plotting utilities for eForge
Version 0.01
+=head1 LICENCE AND COPYRIGHT
+
+Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; version 2 dated June, 1991 or at your option
+any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+A copy of the GNU General Public License is available in the source tree;
+if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+=head1 CONTACT
+
+Charles Breeze, C<< >>
+
+Javier Herrero, C<< >>
+
+=head1 ACKNOWLEDGEMENTS
+
+This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI
+
=cut
+use 5.010;
+use strict;
+use warnings FATAL => 'all';
+use Sort::Naturally;
+
our $VERSION = '0.01';
our (@ISA, @EXPORT, @EXPORT_OK);
@@ -43,7 +71,7 @@ This is the original code using standard R plot to generate a static pdf.
sub Chart{
print "Making static chart.\n";
- my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t1, $t2, $data) = @_;
+ my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t_marginal, $t_strict, $data) = @_;
my $Rdir = $resultsdir;
my $chart = "$lab.chart.pdf";
my $rfile = "$Rdir/$lab.chart.R";
@@ -52,17 +80,17 @@ sub Chart{
open my $rfh, ">", $rfile;
-#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t1, $t2, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3
-$t1 = sprintf("%.2f", $t1);
-$t2 = sprintf("%.2f", $t2);
+#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t_marginal, $t_strict, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3
+$t_marginal = sprintf("%.2f", $t_marginal);
+$t_strict = sprintf("%.2f", $t_strict);
print $rfh "setwd('$Rdir')
results<-read.table('$filename', header=TRUE,sep='\\t')
-# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale)
-results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE)
+# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale)
+results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE)
# Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted)
-results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE)
+results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE)
# Re-order the entries according to tissue first and then cell type/line
tissue.cell.order <- unique(results[, c('Tissue', 'Cell')])
@@ -103,11 +131,11 @@ mtext(2, text='-log10 binomial p-value', line=2, cex=1.4)
# Add legend (internal color first)
palette(c('white', '$msig', '$sig'))
-legend('topleft', pch=19, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white')
+legend('topleft', pch=19, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white')
# Add contour to the points in the legend
palette(c('$ns', '$msig', 'black'))
-legend('topleft', pch=1, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value')
+legend('topleft', pch=1, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value')
palette('default')
dev.off()
@@ -125,7 +153,7 @@ Make dimple interactive chart.
=cut
sub dChart{
- my ($filename, $lab, $resultsdir, $data, $label, $t1, $t2, $web) = @_;
+ my ($filename, $lab, $resultsdir, $data, $label, $t_marginal, $t_strict, $web) = @_;
print "Making dChart.\n";
my $chart = "$lab.dchart.html";
@@ -135,11 +163,22 @@ sub dChart{
print $rcfh "setwd(\"$Rdir\")
results<-read.table(\"$filename\", header = TRUE, sep=\"\\t\")
-# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale)
-results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE)
+# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale)
+results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE)
# Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted)
-results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE)
+results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE)
+color.axis.palette = c();
+if (length(which(results\$Class2 == 1)) > 0 ) {
+ color.axis.palette = c('red');
+}
+if (length(which(results\$Class2 == 2)) > 0 ) {
+ color.axis.palette = c(color.axis.palette, '#FF82ab');
+}
+color.axis.palette = c(color.axis.palette, 'lightblue');
+if (length(color.axis.palette) < 2) {
+ color.axis.palette = c(color.axis.palette, 'lightblue'); # Add it twice to force the color if only non-significant values
+}
results\$log10pvalue <- -log10(results\$Pvalue)
@@ -167,7 +206,7 @@ bounds.width=dplot.width - bounds.x - 20
d1 <- dPlot(
y = 'log10pvalue',
x = c('TissueCell'),
- groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Probe'),
+ groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Datatype', 'Probe'),
data = results,
type = 'bubble',
width = dplot.width,
@@ -186,7 +225,7 @@ d1\$yAxis( type = 'addMeasureAxis' )
d1\$colorAxis(
type = 'addColorAxis',
colorSeries = 'Class2',
- palette = c('red', 'pink', 'lightblue'))
+ palette = color.axis.palette)
# Builds a JS string to add labels for tissues
labels.string = paste(paste0(\"
@@ -298,7 +337,7 @@ sub table{
open my $rcfh, ">", $rfile;
print $rcfh "setwd('$Rdir')
results <- read.table('$filename', header = TRUE, sep='\\t')
-results <- subset(results, T, select = c('Cell', 'Tissue', 'Accession', 'Pvalue', 'Qvalue', 'Probe'))
+results <- subset(results, T, select = c('Cell', 'Tissue', 'Datatype', 'Accession', 'Pvalue', 'Qvalue', 'Probe'))
require(rCharts)
dt <- dTable(
results,
@@ -326,49 +365,4 @@ dt\$save('$chart', cdn = F)\n";
}
}
-
-=head1 AUTHOR
-
-Charles Breeze, C<< >>
-
-=head1 BUGS
-
-Please report any bugs or feature requests to C, or through
-the web interface at L. I will be notified, and then you'll
-automatically be notified of progress on your bug as I make changes.
-
-
-
-
-=head1 SUPPORT
-
-You can find documentation for this module with the perldoc command.
-
- perldoc eForge::ePlot
-
-
-=head1 ACKNOWLEDGEMENTS
-
-
-=head1 LICENSE AND COPYRIGHT
-
-Copyright 2015 Charles Breeze.
-
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; version 2 dated June, 1991 or at your option
-any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-A copy of the GNU General Public License is available in the source tree;
-if not, write to the Free Software Foundation, Inc.,
-51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-
-
-=cut
-
-1; # End of ePlot
+1;
diff --git a/eForge/eStats.pm b/eForge/eStats.pm
index 14421ce..ca6334d 100644
--- a/eForge/eStats.pm
+++ b/eForge/eStats.pm
@@ -1,19 +1,48 @@
package eForge::eStats;
-use 5.010;
-use strict;
-use warnings FATAL => 'all';
-
=head1 NAME
-eStats - Stats for use in eForge
+eForge::eStats - Stats for use in eForge
=head1 VERSION
Version 0.01
+=head1 LICENCE AND COPYRIGHT
+
+Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; version 2 dated June, 1991 or at your option
+any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+A copy of the GNU General Public License is available in the source tree;
+if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+=head1 CONTACT
+
+Charles Breeze, C<< >>
+
+Javier Herrero, C<< >>
+
+=head1 ACKNOWLEDGEMENTS
+
+This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI
+
=cut
+
+use 5.010;
+use strict;
+use warnings FATAL => 'all';
+
our $VERSION = '0.01';
our (@ISA, @EXPORT);
@@ -174,51 +203,4 @@ sub fdr{
}
}
-
-
-
-
-=head1 AUTHOR
-
-Charles Breeze, C<< >>
-
-=head1 BUGS
-#not yet implemented below, it refers to eForge but it is not yet implemented (for cpan) even for Forge
-Please report any bugs or feature requests to C, or through
-the web interface at L. I will be notified, and then you'll
-automatically be notified of progress on your bug as I make changes.
-
-
-
-
-=head1 SUPPORT
-
-You can find documentation for this module with the perldoc command.
-
- perldoc Forge::eStats
-
-
-
-=head1 ACKNOWLEDGEMENTS
-
-
-=head1 LICENSE AND COPYRIGHT
-
-eForge::eStats.pm
-
-Copyright (C) 2015 EMBL - European Bioinformatics Institute and University College London
-
-This program is free software: you can redistribute it and/or modify it under the terms of
-the GNU General Public License as published by the Free Software Foundation, either version 3
-of the License, or (at your option) any later version. This program is distributed in the hope
-that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Neither
-the institution name nor the name eforge.pl can be used to endorse or promote products derived from
-this software without prior written permission. For written permission, please contact
-c.breeze@ucl.ac.uk . Products derived from this software may not be called eforge.pl nor may eforge.pl
-appear in their names without prior written permission of the developers. You should have received
-a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
-
-=cut
-
-1; # End of eStats
+1;
diff --git a/eforge.pl b/eforge.pl
index 9482acb..59914f1 100644
--- a/eforge.pl
+++ b/eforge.pl
@@ -37,6 +37,8 @@ =head1 OPTIONS
Dataset to analyse. Either ENCODE data ('encode'), unconsolidated Roadmap Epigenome data ('erc'), consolidated Roadmap Epigenome data ('erc2'), or Blueprint data ('blueprint'). erc by default.
+Use -data ? to get a list of available datasets on your local install.
+
=item B
Use peaks instead of hotspots. Peaks are more stringent DNase1 peaks calls representing DNase hypersensitive sites,
@@ -48,6 +50,8 @@ =head1 OPTIONS
For the time being, it is suficient for MVPs to be on the 450k array. Probes within 1kb of each other will undergo filtering.
+Use -bkgd ? to get a list of available backgrounds on your local install.
+
=item B