Merge remote-tracking branch 'origin/master' into dgidb-filter

bmeg · Oct 9, 2019 · 0d26221 · 0d26221
2 parents 362d465 + f2f7b30
commit 0d26221
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diff --git a/.dvc/.gitignore b/.dvc/.gitignore
@@ -21,3 +21,4 @@ cache
 /state-wal
 /cache
 /repos
+/tmp
diff --git a/outputs.bmeg_manifest.dvc b/outputs.bmeg_manifest.dvc
@@ -1,4 +1,4 @@
-md5: c6e70ffacb1ef8498c857c749a55daa8
+md5: 3c33eaab693aefe7cfd641283d06d137
 cmd: echo generating file manifest...
 deps:
 - md5: de92fd37fca1bed73a64aa545e422d3a
@@ -65,19 +65,19 @@ deps:
   path: outputs/celllines/Case_SameAs_Case.Edge.json.gz
 - md5: 8e8e11059b5cbd3c1ae85573b30dabb0
   path: outputs/compound/normalized.Case_Compounds_Compound.Edge.json.gz
-- md5: ef8e005a6a56f34904dd4bfd7948355d
+- md5: bb25790bff416d59028c2358b69b03c8
   path: outputs/compound/normalized.Compound.Vertex.json.gz
 - md5: 488eee20c9e4f0c99070eb6dfbb3fdb7
   path: outputs/compound/normalized.Compound_Cases_Case.Edge.json.gz
 - md5: 65e90f12066d8eba49f2a7c6401573d9
   path: outputs/compound/normalized.Compound_DrugResponses_DrugResponse.Edge.json.gz
-- md5: 3a44e58080ed69ba3ac95861a9f6fa67
+- md5: 710e732ae8a92c48204bd5fd33fbcb7c
   path: outputs/compound/normalized.Compound_G2PAssociations_G2PAssociation.Edge.json.gz
 - md5: 8fe1e1cb0721e8d8f8efb46e99ed7514
   path: outputs/compound/normalized.Compound_Projects_Project.Edge.json.gz
 - md5: 9a9fae017188f7f50f06ea922ef085d1
   path: outputs/compound/normalized.DrugResponse_Compounds_Compound.Edge.json.gz
-- md5: 155190bbebf30deaaa01f11c72d3eb22
+- md5: 61bd9cea68e641c69a96269c623c8d73
   path: outputs/compound/normalized.G2PAssociation_Compounds_Compound.Edge.json.gz
 - md5: 5a0a0aa5f5795c2960172004f2aad976
   path: outputs/compound/normalized.Project_Compounds_Compound.Edge.json.gz
@@ -113,15 +113,15 @@ deps:
   path: outputs/ctrp/drug_response.DrugResponse.Vertex.json.gz
 - md5: 50804cc666bd19c2d88baf263890abdd
   path: outputs/ctrp/drug_response.DrugResponse_Aliquot_Aliquot.Edge.json.gz
-- md5: 08f562eb2f651d243650313d27025f19
+- md5: 3fa57b7c369e2c8dd2dc0d0b6c44766e
   path: outputs/dgidb/G2PAssociation.Vertex.json.gz
-- md5: bace58822c69e0b08c338011e2013dfd
+- md5: 166177ce31138f0ee32dc339fdfdd987
   path: outputs/dgidb/G2PAssociation_Genes_Gene.Edge.json.gz
-- md5: 8873040bd458078834079b4963215c6f
+- md5: 4f99308481017576d6cc208b6f514eab
   path: outputs/dgidb/G2PAssociation_Publications_Publication.Edge.json.gz
-- md5: 7f9a0b4f819d366ec099e84b6abbe82c
+- md5: 97282e6b782ab81889884ba6d9ba368e
   path: outputs/dgidb/Gene_G2PAssociations_G2PAssociation.Edge.json.gz
-- md5: 39b8a79b90738115d8912142bd12f71a
+- md5: 03f13f3513d5282b8a1f309429ae81f0
   path: outputs/dgidb/Publication_G2PAssociations_G2PAssociation.Edge.json.gz
 - md5: 3f89bd640983b7ea76b5dbbbcd846941
   path: outputs/ensembl/Exon.Vertex.json.gz
@@ -297,25 +297,25 @@ deps:
   path: outputs/msigdb/Gene_GeneSets_GeneSet.Edge.json.gz
 - md5: 7feb8063bd265b0933cf9d1f7aa7923c
   path: outputs/msigdb/Publication_GeneSets_GeneSet.Edge.json.gz
-- md5: 44b3473c8506169f16ed973e9521c4ad
+- md5: 340814c755cbfc44b71e5c91f5b8df01
   path: outputs/pathway_commons/Gene_InteractionInput_Interaction.Edge.json.gz
-- md5: 5498ed942604fcd735d7aece7c1c4db4
+- md5: 25359033cf924e7031d0780b26d4f75b
   path: outputs/pathway_commons/Gene_Pathways_Pathway.Edge.json.gz
-- md5: ca007c6a34fb336b524ea8f634c5c8b3
+- md5: 377b95536fd909520ded6d189145e665
   path: outputs/pathway_commons/Interaction.Vertex.json.gz
-- md5: 9d4b8673dba5aaec47520f4987467c43
+- md5: 3bcc1bb158d17e20d87dd5339d69ae6e
   path: outputs/pathway_commons/Interaction_InteractionOutput_Gene.Edge.json.gz
-- md5: 239d7afa0017e7b1277dd52ae59fc8de
+- md5: c77dc642d24095dce583d747e61438ef
   path: outputs/pathway_commons/Interaction_Pathways_Pathway.Edge.json.gz
-- md5: a0341597a0aa8a96bcce46d8513ed109
+- md5: 737bc587e7faef80a008f30b9f310643
   path: outputs/pathway_commons/Interaction_Publications_Publication.Edge.json.gz
 - md5: 2f02a1ebb19eafa2d30317429d54b0c6
   path: outputs/pathway_commons/Pathway.Vertex.json.gz
-- md5: 41465ea4b4f7373fccada343cc41b7bd
+- md5: e5b0c497ffd4fe1528f5f7a2cb03909a
   path: outputs/pathway_commons/Pathway_Genes_Gene.Edge.json.gz
-- md5: 32545c213eecf10379d77887bacbaf5b
+- md5: 4342a981012fb96a987efd2e54df9d9b
   path: outputs/pathway_commons/Pathway_Interactions_Interaction.Edge.json.gz
-- md5: 6381ab2738b55712095a487b26d3785d
+- md5: 34ce068f620964c170cc5a297a1f5803
   path: outputs/pathway_commons/Publication_Interactions_Interaction.Edge.json.gz
 - md5: fffda07cbdd2d76010be558a7f6e5b90
   path: outputs/pfam/GeneOntologyTerm_PfamFamilies_PfamFamily.Edge.json.gz

diff --git a/outputs/compound/normalized.compounds.dvc b/outputs/compound/normalized.compounds.dvc
@@ -1,22 +1,24 @@
-md5: 70d7653ce0fa3ae51e3bbb8e49203d6f
+md5: eb52dd28df4a5f37fbafad6164f37584
 cmd: python3 transform/compound/transform.py
 wdir: ../..
 deps:
-- md5: 27eb3c4eae8744024ec3260572db08ee
+- md5: c228b8450fa2537a4acbb4f23f62964f
+  path: source/drug_enricher/drug_alias.tsv
+- md5: 64e7a82c87e7151a7c49846469157547
   path: src/bmeg/enrichers/drug_enricher.py
 - md5: 75929eabe0bb44eee38ad93148a80a41
   path: transform/compound/transform.py
 - md5: b91a5552900b39b0d00ec8c2c2db8faf
   path: outputs/g2p/Compound.Vertex.json.gz
-- md5: ac2dc267e85ae35b42676b63cdfeb03f
+- md5: dd0b9b409000fec9cc7aff13c8413c57
   path: outputs/gdc/gdc.Compound.Vertex.json.gz
 - md5: 5c8cb8428eab4782d8ef1f7c9e150d7d
   path: outputs/ctrp/drug_response.Compound.Vertex.json.gz
 - md5: 187c5b530340c778a45961e7a51ac3e0
   path: outputs/ccle/drug_response.Compound.Vertex.json.gz
 - md5: d0d1f80ac811d6b0bc7b757b02830252
   path: outputs/gdsc/drug_response.Compound.Vertex.json.gz
-- md5: 957bd30274e77148fb5a6d864fc791e4
+- md5: f7a2bbfb7436d76e09b9e13bd3d0c9ff
   path: outputs/dgidb/Compound.Vertex.json.gz
 - md5: 848566e573744e2303b49f6c0986a413
   path: outputs/ccle/drug_response.DrugResponse_Compounds_Compound.Edge.json.gz
@@ -34,13 +36,13 @@ deps:
   path: outputs/g2p/G2PAssociation_Compounds_Compound.Edge.json.gz
 - md5: ea495a03bc6f6c52703487ff94d3ac11
   path: outputs/g2p/Compound_G2PAssociations_G2PAssociation.Edge.json.gz
-- md5: 52fac277f2abf7743b83d145789e48e2
+- md5: 1c2dceb5d39aeda6c06d1099f618548e
   path: outputs/gdc/gdc.Case_Compounds_Compound.Edge.json.gz
-- md5: 2b9bee0cce24df8774c6cd679f23c5fe
+- md5: f0f56a73679667f58b523299bbb4c5b2
   path: outputs/gdc/gdc.Compound_Cases_Case.Edge.json.gz
-- md5: 60e24188073c5032f0d524c7ac0e1599
+- md5: a9ee2034b226d6900855e32a450dfb18
   path: outputs/gdc/gdc.Compound_Projects_Project.Edge.json.gz
-- md5: 088dad4200a6eadc0ad86b3015948648
+- md5: 8353be3aeae5722664f0e6691af525f6
   path: outputs/gdc/gdc.Project_Compounds_Compound.Edge.json.gz
 - md5: 7e78ec6311fca7f7d13bb8b1cdb74b91
   path: outputs/ccle/drug_response.Project_Compounds_Compound.Edge.json.gz
@@ -54,52 +56,52 @@ deps:
   path: outputs/gdsc/drug_response.Project_Compounds_Compound.Edge.json.gz
 - md5: 991c580d8354294781105155bf773d88
   path: outputs/gdsc/drug_response.Compound_Projects_Project.Edge.json.gz
-- md5: 03e3518d725df7eceb5996fedbf2073d
+- md5: 9c4627785660215fa9adbf7c9f6cf172
   path: outputs/dgidb/G2PAssociation_Compounds_Compound.Edge.json.gz
-- md5: 068131a8e65c05bb509d273a776e2554
+- md5: fa0ae005deb28af2d935cc818c1394b4
   path: outputs/dgidb/Compound_G2PAssociations_G2PAssociation.Edge.json.gz
 outs:
-- md5: 0a5cd11e0f91ca8da6ce769942b5814e
+- md5: bb25790bff416d59028c2358b69b03c8
   path: outputs/compound/normalized.Compound.Vertex.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 086ef043be327bb1694204d9739fb318
+- md5: 9a9fae017188f7f50f06ea922ef085d1
   path: outputs/compound/normalized.DrugResponse_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 37ec1a8da6c0602b01e54596e7cf52fb
+- md5: 65e90f12066d8eba49f2a7c6401573d9
   path: outputs/compound/normalized.Compound_DrugResponses_DrugResponse.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 4083e6035935fe8d19715d16f340bb13
+- md5: 5a0a0aa5f5795c2960172004f2aad976
   path: outputs/compound/normalized.Project_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 65f668e75679d68b86882d815f4f27de
+- md5: 8fe1e1cb0721e8d8f8efb46e99ed7514
   path: outputs/compound/normalized.Compound_Projects_Project.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 1283639410fda8478d05e5bedf02ade0
+- md5: 488eee20c9e4f0c99070eb6dfbb3fdb7
   path: outputs/compound/normalized.Compound_Cases_Case.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 01a7c9c9d89170faf93b9d05557e3945
+- md5: 8e8e11059b5cbd3c1ae85573b30dabb0
   path: outputs/compound/normalized.Case_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: b96ce39187eefa958e9b92e0a36e1f3f
+- md5: 61bd9cea68e641c69a96269c623c8d73
   path: outputs/compound/normalized.G2PAssociation_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 300b73f60897b6c68b24b394b7781e10
+- md5: 710e732ae8a92c48204bd5fd33fbcb7c
   path: outputs/compound/normalized.Compound_G2PAssociations_G2PAssociation.Edge.json.gz
   cache: true
   metric: false

diff --git a/outputs/dgidb/dgidb.dvc b/outputs/dgidb/dgidb.dvc
@@ -1,52 +1,52 @@
-md5: e5c5c7205616731514966f5f7b3d74c4
+md5: e720598cc16fd7bb5918bd09f0397589
 cmd: python3 transform/dgidb/transform.py
 wdir: ../..
 deps:
 - md5: 7adcf4f9a4580908139f3e16877003f3
   path: source/dgidb/interactions.tsv
-- md5: 8a36c7915e0fefdc2d8deec16b883802
+- md5: c228b8450fa2537a4acbb4f23f62964f
   path: source/drug_enricher/drug_alias.tsv
-- md5: 27eb3c4eae8744024ec3260572db08ee
+- md5: 64e7a82c87e7151a7c49846469157547
   path: src/bmeg/enrichers/drug_enricher.py
 - md5: 936873de1ea7a748293263ff126a2967
   path: transform/dgidb/transform.py
 outs:
-- md5: 08f562eb2f651d243650313d27025f19
+- md5: 3fa57b7c369e2c8dd2dc0d0b6c44766e
   path: outputs/dgidb/G2PAssociation.Vertex.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 0bd6b1df399d8557ce48d4836886a2c3
+- md5: f7a2bbfb7436d76e09b9e13bd3d0c9ff
   path: outputs/dgidb/Compound.Vertex.json.gz
   cache: true
   metric: false
   persist: false
-- md5: bace58822c69e0b08c338011e2013dfd
+- md5: 166177ce31138f0ee32dc339fdfdd987
   path: outputs/dgidb/G2PAssociation_Genes_Gene.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 8873040bd458078834079b4963215c6f
+- md5: 4f99308481017576d6cc208b6f514eab
   path: outputs/dgidb/G2PAssociation_Publications_Publication.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 5046608b07201c85d11907303c1cb507
+- md5: 9c4627785660215fa9adbf7c9f6cf172
   path: outputs/dgidb/G2PAssociation_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 39b8a79b90738115d8912142bd12f71a
+- md5: 03f13f3513d5282b8a1f309429ae81f0
   path: outputs/dgidb/Publication_G2PAssociations_G2PAssociation.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 7f9a0b4f819d366ec099e84b6abbe82c
+- md5: 97282e6b782ab81889884ba6d9ba368e
   path: outputs/dgidb/Gene_G2PAssociations_G2PAssociation.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: ce10deaafb0d2bef94c8256c9c356571
+- md5: fa0ae005deb28af2d935cc818c1394b4
   path: outputs/dgidb/Compound_G2PAssociations_G2PAssociation.Edge.json.gz
   cache: true
   metric: false

diff --git a/outputs/gdc/compounds.dvc b/outputs/gdc/compounds.dvc
@@ -1,33 +1,33 @@
-md5: 45858638077daeac8195974c0b009d6a
+md5: f76a0dbff3cd7b9155bb45d0640c3aae
 cmd: python3 transform/gdc/compounds.py
 wdir: ../..
 deps:
-- md5: 3671d627cbd0d175e928c2183c8246db
+- md5: 8da7c4b8dc2e733e563edeb4121ad770
   path: transform/gdc/compounds.py
 - md5: 52c1659f52406869466253844f48fe1c.dir
   path: source/gdc/compounds
 outs:
-- md5: ac2dc267e85ae35b42676b63cdfeb03f
+- md5: dd0b9b409000fec9cc7aff13c8413c57
   path: outputs/gdc/gdc.Compound.Vertex.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 52fac277f2abf7743b83d145789e48e2
+- md5: 1c2dceb5d39aeda6c06d1099f618548e
   path: outputs/gdc/gdc.Case_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 2b9bee0cce24df8774c6cd679f23c5fe
+- md5: f0f56a73679667f58b523299bbb4c5b2
   path: outputs/gdc/gdc.Compound_Cases_Case.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 60e24188073c5032f0d524c7ac0e1599
+- md5: a9ee2034b226d6900855e32a450dfb18
   path: outputs/gdc/gdc.Compound_Projects_Project.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 088dad4200a6eadc0ad86b3015948648
+- md5: 8353be3aeae5722664f0e6691af525f6
   path: outputs/gdc/gdc.Project_Compounds_Compound.Edge.json.gz
   cache: true
   metric: false

diff --git a/outputs/pathway_commons/pc11.dvc b/outputs/pathway_commons/pc11.dvc
@@ -1,11 +1,11 @@
-md5: a15b17e58e79361cd91ea24c40b4f6dd
+md5: ab8f13798f8cec247ccb51755bcb046f
 cmd: python3 transform/pathway_commons/transform.py
 wdir: ../..
 deps:
-- md5: acd261436174e4691808cbc392c42b0d
+- md5: f505dcb35fee063eeaf2491b4446b8ac
   path: transform/pathway_commons/transform.py
-- md5: dc1de915f00c5d7b37cfe7cd57b2f2b8
-  path: source/pathway_commons/pc11.detailed.sif
+- md5: 388d4680850f9ab3c24a9036f0b1c530
+  path: source/pathway_commons/pc11.all.sif
 - md5: 475d63e91f5e1a7af2b36233dc462a56
   path: source/pathway_commons/pathways.txt.gz
 outs:
@@ -14,47 +14,47 @@ outs:
   cache: true
   metric: false
   persist: false
-- md5: ca007c6a34fb336b524ea8f634c5c8b3
+- md5: 377b95536fd909520ded6d189145e665
   path: outputs/pathway_commons/Interaction.Vertex.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 44b3473c8506169f16ed973e9521c4ad
+- md5: 340814c755cbfc44b71e5c91f5b8df01
   path: outputs/pathway_commons/Gene_InteractionInput_Interaction.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 5498ed942604fcd735d7aece7c1c4db4
+- md5: 25359033cf924e7031d0780b26d4f75b
   path: outputs/pathway_commons/Gene_Pathways_Pathway.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 9d4b8673dba5aaec47520f4987467c43
+- md5: 3bcc1bb158d17e20d87dd5339d69ae6e
   path: outputs/pathway_commons/Interaction_InteractionOutput_Gene.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 239d7afa0017e7b1277dd52ae59fc8de
+- md5: c77dc642d24095dce583d747e61438ef
   path: outputs/pathway_commons/Interaction_Pathways_Pathway.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: a0341597a0aa8a96bcce46d8513ed109
+- md5: 737bc587e7faef80a008f30b9f310643
   path: outputs/pathway_commons/Interaction_Publications_Publication.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 41465ea4b4f7373fccada343cc41b7bd
+- md5: e5b0c497ffd4fe1528f5f7a2cb03909a
   path: outputs/pathway_commons/Pathway_Genes_Gene.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 32545c213eecf10379d77887bacbaf5b
+- md5: 4342a981012fb96a987efd2e54df9d9b
   path: outputs/pathway_commons/Pathway_Interactions_Interaction.Edge.json.gz
   cache: true
   metric: false
   persist: false
-- md5: 6381ab2738b55712095a487b26d3785d
+- md5: 34ce068f620964c170cc5a297a1f5803
   path: outputs/pathway_commons/Publication_Interactions_Interaction.Edge.json.gz
   cache: true
   metric: false

diff --git a/source/drug_enricher/drug_alias.tsv b/source/drug_enricher/drug_alias.tsv
@@ -1129,7 +1129,6 @@ methotrexate+5 fluorouracil+cyclophosphamide	Methotrexate+Fluorouracil+Cyclophos
 metilprednisona	Methylprednisolone
 metotreksat	Methotrexate
 nab-rapamycin	Rapamycin
-name	alias
 navelbine	Vinorelbine
 neulasta	Pegfilgrastim
 nolvadex	Tamoxifen
@@ -1144,7 +1143,6 @@ pemetrexed disodium	Pemetrexed
 prednisona	Prednisone
 premetrexed	Pemetrexed
 proleukin (IL-2)	Aldesleukin
-rTRAIL	trail blazers
 rec MAGE	MAGE-3-AS-AS15-ASCI
 rec MAGE 3-AS + AS15 ACS1 / Placebo Vaccine	MAGE-3-AS-AS15-ASCI
 rec MAGE3-AS+AS15 ASCI vs Placebo	MAGE-3-AS-AS15-ASCI

diff --git a/source/pathway_commons/.gitignore b/source/pathway_commons/.gitignore
@@ -1,3 +1,4 @@
 /pc11.detailed.sif
 /pathways.txt.gz
 /pathways.txt
+/pc11.all.sif
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,3 +21,4 @@ cache @@
     /state-wal
     /cache
     /repos
+    /tmp