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Merge pull request #354 from at7/fix/add_missing_funcgen_patches_95
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Fix/add missing funcgen patches 95
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@helensch
helensch committed Dec 20, 2018
2 parents d828487 + 11ec9c1 commit d7e1659
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Showing 9 changed files with 157 additions and 123 deletions.
42 changes: 21 additions & 21 deletions t/AnnotationSource_Database_RegFeat.t
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Expand Up @@ -88,43 +88,43 @@ SKIP: {
$as->get_available_cell_types,
[
'A549',
'CD14+CD16-_monocyte_(CB)',
'CD14+CD16-_monocyte_(VB)',
'CD4+_ab_T_cell_(VB)',
'CD8+_ab_T_cell_(CB)',
'CM_CD4+_ab_T_cell_(VB)',
'CD14+CD16-Monocyte:CordBlood:hist',
'CD14+CD16-Monocyte:VenousBlood:hist',
'CD4+abTcell:VenousBlood:hist',
'CD8+abTcell:CordBlood:hist',
'CMCD4+abTcell:VenousBlood:hist',
'DND-41',
'EPC_(VB)',
'EPC:VenousBlood:hist',
'GM12878',
'H1ESC',
'HMEC',
'HSMM',
'HSMMtube',
'HUVEC',
'HUVEC_prol_(CB)',
'HUVECprol:CordBlood:hist',
'HeLa-S3',
'HepG2',
'IMR90',
'K562',
'M0_macrophage_(CB)',
'M0_macrophage_(VB)',
'M1_macrophage_(CB)',
'M1_macrophage_(VB)',
'M2_macrophage_(CB)',
'M2_macrophage_(VB)',
'MSC_(VB)',
'M0Macrophage:CordBlood:hist',
'M0Macrophage:VenousBlood:hist',
'M1Macrophage:CordBlood:hist',
'M1Macrophage:VenousBlood:hist',
'M2Macrophage:CordBlood:hist',
'M2Macrophage:VenousBlood:hist',
'MSC:VenousBlood:hist',
'Monocytes-CD14+',
'NH-A',
'NHDF-Ad',
'NHDF-AD',
'NHEK',
'NHLF',
'Osteobl',
'eosinophil_(VB)',
'erythroblast_(CB)',
'naive_B_cell_(VB)',
'neutro_myelocyte_(BM)',
'neutrophil_(CB)',
'neutrophil_(VB)'
'eosinophil:VenousBlood:hist',
'erythroblast:CordBlood:hist',
'naiveBcell:VenousBlood:hist',
'neutroMyelocyte:BoneMarrow:hist',
'neutrophil:CordBlood:hist',
'neutrophil:VenousBlood:hist'
],
'get_available_cell_types - empty'
);
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68 changes: 34 additions & 34 deletions t/test-genome-DBs/homo_vepiens/funcgen/epigenome.txt
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Expand Up @@ -72,7 +72,7 @@
76 NHBE NHBE Normal Human Bronchial Epithelial Cells NHBE unknown
77 NHDF-neo NHDF-neo Neonatal Human Dermal Fibroblasts NHDF_neo unknown
78 NHLF NHLF Normal Human Long Fibroblasts NHLF unknown
79 NT2-D1 NTERA-2 cl.D1 Malignant Pluripotent Testicular Embryonal Carcinoma NT2_D1 male
79 NT2-D1 NT2-D1 Malignant Pluripotent Testicular Embryonal Carcinoma NT2_D1 male
80 Panc1 Panc1 Pancreatic Carcinoma Panc1 unknown
81 PanIslets PanIslets Human Pancreatic Islets PanIslets male
82 PFSK1 PFSK1 Neurectodermal cell line PFSK1 male
Expand All @@ -92,38 +92,38 @@
96 Fibrobl Fibrobl Child Fibroblast Fibrobl female
97 GM12878-XiMat GM12878-XiMat Lymphoblastoid, Epstein-Barr Virus, Cloned for maternal X inactivation GM12878_XiMat female
98 BJ BJ Foreskin fibroblast BJ male
102 NHDF-AD NHDF-Ad adult dermal fibroblasts NHDF_AD female
102 NHDF-AD NHDF-AD adult dermal fibroblasts NHDF_AD female
103 Monocytes-CD14+ Monocytes-CD14+ CD14-positive cells human leukapheresis production Monocytes_CD14 female
240 DND-41 DND-41 Human leukemic T-cell line with p53 (Notch) mutation DND_41 male
241 M1Macrophage:VenousBlood:hist M1 macrophage (VB) M1 macrophage from Venous Blood M1Macrophage_VenousBlood_hist mixed
242 CD4+abTcell:CordBlood:hist CD4+ ab T cell (CB) CD4+ ab T cell from Cord Blood CD4abTcell_CordBlood_hist mixed
243 erythroblast:CordBlood:hist erythroblast (CB) erythroblast from Cord Blood erythroblast_CordBlood_hist mixed
244 M1Macrophage:CordBlood:hist M1 macrophage (CB) M1 macrophage from Cord Blood M1Macrophage_CordBlood_hist mixed
245 eosinophil:VenousBlood:hist eosinophil (VB) eosinophil from Venous Blood eosinophil_VenousBlood_hist mixed
246 M0Macrophage:CordBlood:hist M0 macrophage (CB) M0 macrophage from Cord Blood M0Macrophage_CordBlood_hist mixed
247 CD14+CD16-Monocyte:VenousBlood:dnase CD14+CD16- monocyte (VB) CD14+ CD16- monocyte from Venous Blood CD14CD16_Monocyte_VenousBlood_dnase mixed
248 CD14+CD16-Monocyte:VenousBlood:hist CD14+CD16- monocyte (VB) CD14+ CD16- monocyte from Venous Blood CD14CD16_Monocyte_VenousBlood_hist mixed
249 CD8+abTcell:CordBlood:hist CD8+ ab T cell (CB) CD8+ ab T cell from Cord Blood CD8abTcell_CordBlood_hist mixed
250 CD8+abTcell:VenousBlood:hist CD8+ ab T cell (VB) CD8+ ab T cell from Venous Blood CD8abTcell_VenousBlood_hist mixed
251 CD38-naiveBcell:VenousBlood:hist CD38- naive B cell (VB) CD38- naive B cell from Venous Blood CD38_naiveBcell_VenousBlood_hist mixed
252 naiveBcell:VenousBlood:hist naive B cell (VB) naive B cell from Venous Blood naiveBcell_VenousBlood_hist mixed
253 HUVECprol:CordBlood:hist HUVEC prol (CB) HUVEC prol from Cord Blood HUVECprol_CordBlood_hist mixed
254 CMCD4+abTcell:VenousBlood:hist CM CD4+ ab T cell (VB) CM CD4+ ab T cell from Venous Blood CMCD4abTcell_VenousBlood_hist mixed
255 CD38-naiveBcell:CordBlood:hist CD38- naive B cell (CB) CD38- naive B cell from Cord Blood CD38_naiveBcell_CordBlood_hist mixed
256 M0Macrophage:VenousBlood:hist M0 macrophage (VB) M0 macrophage from Venous Blood M0Macrophage_VenousBlood_hist mixed
257 MSC:VenousBlood:hist MSC (VB) MSC from Venous Blood MSC_VenousBlood_hist mixed
258 neutrophil:CordBlood:hist neutrophil (CB) neutrophil from Cord Blood neutrophil_CordBlood_hist mixed
259 EPC:VenousBlood:hist EPC (VB) EPC from Venous Blood EPC_VenousBlood_hist mixed
260 naiveBcell:Tonsil:hist naive B cell (To) naive B cell from Tonsil naiveBcell_Tonsil_hist mixed
261 EMCD8+abTcell:VenousBlood:hist CM CD4+ ab T cell (VB) EM CD8+ ab T cell from Venous Blood EMCD8abTcell_VenousBlood_hist mixed
262 M2Macrophage:VenousBlood:hist M2 macrophage (VB) M2 macrophage from Venous Blood M2Macrophage_VenousBlood_hist mixed
263 M1Macrophage:VenousBlood:dnase M1 macrophage (VB) M1 macrophage from Venous Blood M1Macrophage_VenousBlood_dnase mixed
264 CD14+CD16-Monocyte:CordBlood:hist CD14+CD16- monocyte (CB) CD14+ CD16- monocyte from Cord Blood CD14CD16_Monocyte_CordBlood_hist mixed
265 neutrophil:VenousBlood:hist neutrophil (VB) neutrophil from Venous Blood neutrophil_VenousBlood_hist mixed
266 neutroMyelocyte:BoneMarrow:hist neutro myelocyte (BM) neutro myelocyte from Bone Marrow neutroMyelocyte_BoneMarrow_hist mixed
267 M2Macrophage:CordBlood:hist M2 macrophage (CB) M2 macrophage from Cord Blood M2Macrophage_CordBlood_hist mixed
268 M0Macrophage:VenousBlood:dnase M0 macrophage (VB) M0 macrophage from Venous Blood M0Macrophage_VenousBlood_dnase mixed
269 M2Macrophage:VenousBlood:dnase M2 macrophage (VB) M2 macrophage from Venous Blood M2Macrophage_VenousBlood_dnase mixed
270 CD14+CD16-Monocyte:CordBlood:dnase CD14+CD16- monocyte (CB) CD14+ CD16- monocyte from Cord Blood CD14CD16_Monocyte_CordBlood_dnase mixed
271 CD4+abTcell:VenousBlood:hist CD4+ ab T cell (VB) CD4+ ab T cell from Venous Blood CD4abTcell_VenousBlood_hist mixed
272 CD8+abTcell:CordBlood:dnase CD8+ ab T cell (CB) CD8+ ab T cell from Cord Blood CD8abTcell_CordBlood_dnase mixed
241 M1Macrophage:VenousBlood:hist M1Macrophage:VenousBlood:hist M1 macrophage from Venous Blood M1Macrophage_VenousBlood_hist mixed
242 CD4+abTcell:CordBlood:hist CD4+abTcell:CordBlood:hist CD4+ ab T cell from Cord Blood CD4abTcell_CordBlood_hist mixed
243 erythroblast:CordBlood:hist erythroblast:CordBlood:hist erythroblast from Cord Blood erythroblast_CordBlood_hist mixed
244 M1Macrophage:CordBlood:hist M1Macrophage:CordBlood:hist M1 macrophage from Cord Blood M1Macrophage_CordBlood_hist mixed
245 eosinophil:VenousBlood:hist eosinophil:VenousBlood:hist eosinophil from Venous Blood eosinophil_VenousBlood_hist mixed
246 M0Macrophage:CordBlood:hist M0Macrophage:CordBlood:hist M0 macrophage from Cord Blood M0Macrophage_CordBlood_hist mixed
247 CD14+CD16-Monocyte:VenousBlood:dnase CD14+CD16-Monocyte:VenousBlood:dnase CD14+ CD16- monocyte from Venous Blood CD14CD16_Monocyte_VenousBlood_dnase mixed
248 CD14+CD16-Monocyte:VenousBlood:hist CD14+CD16-Monocyte:VenousBlood:hist CD14+ CD16- monocyte from Venous Blood CD14CD16_Monocyte_VenousBlood_hist mixed
249 CD8+abTcell:CordBlood:hist CD8+abTcell:CordBlood:hist CD8+ ab T cell from Cord Blood CD8abTcell_CordBlood_hist mixed
250 CD8+abTcell:VenousBlood:hist CD8+abTcell:VenousBlood:hist CD8+ ab T cell from Venous Blood CD8abTcell_VenousBlood_hist mixed
251 CD38-naiveBcell:VenousBlood:hist CD38-naiveBcell:VenousBlood:hist CD38- naive B cell from Venous Blood CD38_naiveBcell_VenousBlood_hist mixed
252 naiveBcell:VenousBlood:hist naiveBcell:VenousBlood:hist naive B cell from Venous Blood naiveBcell_VenousBlood_hist mixed
253 HUVECprol:CordBlood:hist HUVECprol:CordBlood:hist HUVEC prol from Cord Blood HUVECprol_CordBlood_hist mixed
254 CMCD4+abTcell:VenousBlood:hist CMCD4+abTcell:VenousBlood:hist CM CD4+ ab T cell from Venous Blood CMCD4abTcell_VenousBlood_hist mixed
255 CD38-naiveBcell:CordBlood:hist CD38-naiveBcell:CordBlood:hist CD38- naive B cell from Cord Blood CD38_naiveBcell_CordBlood_hist mixed
256 M0Macrophage:VenousBlood:hist M0Macrophage:VenousBlood:hist M0 macrophage from Venous Blood M0Macrophage_VenousBlood_hist mixed
257 MSC:VenousBlood:hist MSC:VenousBlood:hist MSC from Venous Blood MSC_VenousBlood_hist mixed
258 neutrophil:CordBlood:hist neutrophil:CordBlood:hist neutrophil from Cord Blood neutrophil_CordBlood_hist mixed
259 EPC:VenousBlood:hist EPC:VenousBlood:hist EPC from Venous Blood EPC_VenousBlood_hist mixed
260 naiveBcell:Tonsil:hist naiveBcell:Tonsil:hist naive B cell from Tonsil naiveBcell_Tonsil_hist mixed
261 EMCD8+abTcell:VenousBlood:hist EMCD8+abTcell:VenousBlood:hist EM CD8+ ab T cell from Venous Blood EMCD8abTcell_VenousBlood_hist mixed
262 M2Macrophage:VenousBlood:hist M2Macrophage:VenousBlood:hist M2 macrophage from Venous Blood M2Macrophage_VenousBlood_hist mixed
263 M1Macrophage:VenousBlood:dnase M1Macrophage:VenousBlood:dnase M1 macrophage from Venous Blood M1Macrophage_VenousBlood_dnase mixed
264 CD14+CD16-Monocyte:CordBlood:hist CD14+CD16-Monocyte:CordBlood:hist CD14+ CD16- monocyte from Cord Blood CD14CD16_Monocyte_CordBlood_hist mixed
265 neutrophil:VenousBlood:hist neutrophil:VenousBlood:hist neutrophil from Venous Blood neutrophil_VenousBlood_hist mixed
266 neutroMyelocyte:BoneMarrow:hist neutroMyelocyte:BoneMarrow:hist neutro myelocyte from Bone Marrow neutroMyelocyte_BoneMarrow_hist mixed
267 M2Macrophage:CordBlood:hist M2Macrophage:CordBlood:hist M2 macrophage from Cord Blood M2Macrophage_CordBlood_hist mixed
268 M0Macrophage:VenousBlood:dnase M0Macrophage:VenousBlood:dnase M0 macrophage from Venous Blood M0Macrophage_VenousBlood_dnase mixed
269 M2Macrophage:VenousBlood:dnase M2Macrophage:VenousBlood:dnase M2 macrophage from Venous Blood M2Macrophage_VenousBlood_dnase mixed
270 CD14+CD16-Monocyte:CordBlood:dnase CD14+CD16-Monocyte:CordBlood:dnase CD14+ CD16- monocyte from Cord Blood CD14CD16_Monocyte_CordBlood_dnase mixed
271 CD4+abTcell:VenousBlood:hist CD4+abTcell:VenousBlood:hist CD4+ ab T cell from Venous Blood CD4abTcell_VenousBlood_hist mixed
272 CD8+abTcell:CordBlood:dnase CD8+abTcell:CordBlood:dnase CD8+ ab T cell from Cord Blood CD8abTcell_CordBlood_dnase mixed
8 changes: 4 additions & 4 deletions t/test-genome-DBs/homo_vepiens/funcgen/experimental_group.txt
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@@ -1,4 +1,4 @@
2 ENCODE \N \N The ENCODE Project http://encodeproject.org 1
3 Roadmap Epigenomics \N \N The NIH Roadmap Epigenomics Mapping Consortium http://www.roadmapepigenomics.org/ 1
4 Publication \N \N Manual Curation from a Publication \N 0
5 BLUEPRINT \N \N A BLUEPRINT of Haematopoietic Epigenomes http://www.blueprint-epigenome.eu/ 1
2 ENCODE encode The ENCODE Project http://encodeproject.org 1
3 Roadmap Epigenomics roadmap_epigenomics The NIH Roadmap Epigenomics Mapping Consortium http://www.roadmapepigenomics.org/ 1
4 Publication publication Manual Curation from a Publication \N 0
5 BLUEPRINT blueprint A BLUEPRINT of Haematopoietic Epigenomes http://www.blueprint-epigenome.eu/ 1
13 changes: 13 additions & 0 deletions t/test-genome-DBs/homo_vepiens/funcgen/meta.txt
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Expand Up @@ -291,3 +291,16 @@
735 \N patch patch_93_94_l.sql|Modify binding_matrix_table
736 \N patch patch_93_94_m.sql|Create binding_matrix_frequencies table
737 \N patch patch_94_95_a.sql|schema_version
738 \N patch patch_94_95_b.sql|update to segmentation state tables
739 \N patch patch_94_95_c.sql|Update to alignment table
740 \N patch patch_94_95_d.sql|Update to execution_plan table
741 \N patch patch_94_95_e.sql|Update to regulatory_build_statistic table
742 \N patch patch_94_95_f.sql|Update to experimental_group table
743 \N patch patch_94_95_g.sql|segmentation table
744 \N patch patch_94_95_h.sql|segmentation_cell_tables
745 \N patch patch_94_95_i.sql|segmentation_statistic table
746 \N patch patch_94_95_j.sql|segmentation_file table
747 \N patch patch_94_95_k.sql|peak calling statistic table
748 \N patch patch_94_95_l.sql|Modify length for column name from epigenome table
749 \N patch patch_94_95_m.sql|drop obsolete tables
750 \N patch patch_94_95_n.sql|add unique constrain on display_label column for epigenome table
Empty file added t/test-genome-DBs/homo_vepiens/funcgen/segmentation.txt
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Empty file added t/test-genome-DBs/homo_vepiens/funcgen/segmentation_cell_tables.txt
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76 changes: 38 additions & 38 deletions t/test-genome-DBs/homo_vepiens/funcgen/segmentation_file.txt
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@@ -1,38 +1,38 @@
1 1 NHA.bb 77 21
2 1 NHEK.bb 77 17
3 1 A549.bb 77 24
4 1 M2MACROPHAGExVENOUSBLOODxHIST.bb 73 262
5 1 HUVEC.bb 77 16
6 1 HUVECPROLxCORDBLOODxHIST.bb 73 253
7 1 EPCxVENOUSBLOODxHIST.bb 73 259
8 1 M2MACROPHAGExCORDBLOODxHIST.bb 73 267
9 1 NEUTROPHILxCORDBLOODxHIST.bb 73 258
10 1 HSMMTUBE.bb 77 92
11 1 MSCxVENOUSBLOODxHIST.bb 73 257
12 1 IMR90.bb 77 5
13 1 K562.bb 77 14
14 1 NHLF.bb 77 78
15 1 NEUTROMYELOCYTExBONEMARROWxHIST.bb 73 266
16 1 M0MACROPHAGExCORDBLOODxHIST.bb 73 246
17 1 OSTEOBL.bb 77 93
18 1 CD8+ABTCELLxCORDBLOODxHIST.bb 73 249
19 1 DND41.bb 77 240
20 1 HELAS3.bb 77 1
21 1 NEUTROPHILxVENOUSBLOODxHIST.bb 73 265
22 1 HSMM.bb 77 22
23 1 EOSINOPHILxVENOUSBLOODxHIST.bb 73 245
24 1 H1ESC.bb 77 18
25 1 HMEC.bb 77 23
26 1 M1MACROPHAGExCORDBLOODxHIST.bb 73 244
27 1 MONOCYTESCD14+.bb 77 103
28 1 ERYTHROBLASTxCORDBLOODxHIST.bb 73 243
29 1 M0MACROPHAGExVENOUSBLOODxHIST.bb 73 256
30 1 CMCD4+ABTCELLxVENOUSBLOODxHIST.bb 73 254
31 1 NAIVEBCELLxVENOUSBLOODxHIST.bb 73 252
32 1 GM12878.bb 77 15
33 1 M1MACROPHAGExVENOUSBLOODxHIST.bb 73 241
34 1 CD14+CD16MONOCYTExVENOUSBLOODxHIST.bb 73 248
35 1 NHDFAD.bb 77 102
36 1 HEPG2.bb 77 7
37 1 CD14+CD16MONOCYTExCORDBLOODxHIST.bb 73 264
38 1 CD4+ABTCELLxVENOUSBLOODxHIST.bb 73 271
1 1 NHA.bb 77 21 \N
2 1 NHEK.bb 77 17 \N
3 1 A549.bb 77 24 \N
4 1 M2MACROPHAGExVENOUSBLOODxHIST.bb 73 262 \N
5 1 HUVEC.bb 77 16 \N
6 1 HUVECPROLxCORDBLOODxHIST.bb 73 253 \N
7 1 EPCxVENOUSBLOODxHIST.bb 73 259 \N
8 1 M2MACROPHAGExCORDBLOODxHIST.bb 73 267 \N
9 1 NEUTROPHILxCORDBLOODxHIST.bb 73 258 \N
10 1 HSMMTUBE.bb 77 92 \N
11 1 MSCxVENOUSBLOODxHIST.bb 73 257 \N
12 1 IMR90.bb 77 5 \N
13 1 K562.bb 77 14 \N
14 1 NHLF.bb 77 78 \N
15 1 NEUTROMYELOCYTExBONEMARROWxHIST.bb 73 266 \N
16 1 M0MACROPHAGExCORDBLOODxHIST.bb 73 246 \N
17 1 OSTEOBL.bb 77 93 \N
18 1 CD8+ABTCELLxCORDBLOODxHIST.bb 73 249 \N
19 1 DND41.bb 77 240 \N
20 1 HELAS3.bb 77 1 \N
21 1 NEUTROPHILxVENOUSBLOODxHIST.bb 73 265 \N
22 1 HSMM.bb 77 22 \N
23 1 EOSINOPHILxVENOUSBLOODxHIST.bb 73 245 \N
24 1 H1ESC.bb 77 18 \N
25 1 HMEC.bb 77 23 \N
26 1 M1MACROPHAGExCORDBLOODxHIST.bb 73 244 \N
27 1 MONOCYTESCD14+.bb 77 103 \N
28 1 ERYTHROBLASTxCORDBLOODxHIST.bb 73 243 \N
29 1 M0MACROPHAGExVENOUSBLOODxHIST.bb 73 256 \N
30 1 CMCD4+ABTCELLxVENOUSBLOODxHIST.bb 73 254 \N
31 1 NAIVEBCELLxVENOUSBLOODxHIST.bb 73 252 \N
32 1 GM12878.bb 77 15 \N
33 1 M1MACROPHAGExVENOUSBLOODxHIST.bb 73 241 \N
34 1 CD14+CD16MONOCYTExVENOUSBLOODxHIST.bb 73 248 \N
35 1 NHDFAD.bb 77 102 \N
36 1 HEPG2.bb 77 7 \N
37 1 CD14+CD16MONOCYTExCORDBLOODxHIST.bb 73 264 \N
38 1 CD4+ABTCELLxVENOUSBLOODxHIST.bb 73 271 \N
Empty file added t/test-genome-DBs/homo_vepiens/funcgen/segmentation_statistic.txt
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