From 71efcfc8c24addddfae79cd08451369c64b335f2 Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Thu, 7 Apr 2016 18:11:40 +0100 Subject: [PATCH] Adding blueprint data for eforge v1.2 --- database/README.txt | 27 ++++++++++---------- database/blueprint.decode | 60 ++++++++++++++++++++++----------------------- database/load_450k_array.pl | 2 +- database/load_dataset.pl | 3 ++- 4 files changed, 47 insertions(+), 45 deletions(-) diff --git a/database/README.txt b/database/README.txt index 9c09a8b..2e53347 100755 --- a/database/README.txt +++ b/database/README.txt @@ -10,29 +10,30 @@ In summary, the steps are: Please refer to the help of init_db.pl for information about the different options -rm eforge_1.1.db -perl init_db.pl --db_name eforge_1.1.db +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 +perl load_450k_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_1.1.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ -perl load_dataset.pl --db_name eforge_1.1.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.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_1.1.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_1.1.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_1.1.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_1.1.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_1.1.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 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_1.1.db .. +mv eforge_1.2.db .. diff --git a/database/blueprint.decode b/database/blueprint.decode index f498876..eb41245 100644 --- a/database/blueprint.decode +++ b/database/blueprint.decode @@ -1,31 +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/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -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/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -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/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -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/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS -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/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -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/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -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/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -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/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS -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/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS -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/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS -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/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -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/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS +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/load_450k_array.pl b/database/load_450k_array.pl index 65ff62d..cde3c49 100644 --- a/database/load_450k_array.pl +++ b/database/load_450k_array.pl @@ -7,7 +7,7 @@ use DBI; my $db_dir = "."; -my $db_name = "eforge_1.1.db"; +my $db_name = "eforge_1.2.db"; my $array_tag = "450k"; my $array_name = "Illumina Human 450k array"; my $species = "Homo sapiens"; diff --git a/database/load_dataset.pl b/database/load_dataset.pl index c984b0c..6c947d3 100644 --- a/database/load_dataset.pl +++ b/database/load_dataset.pl @@ -238,7 +238,8 @@ sub get_decode_table { $decode_record->{$header[$i]} = $data[$i]; } # Check that file and URL match - die $this_line if ($decode_record->{"url"} !~ $decode_record->{"file"}); + die "File: ".$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);