rbbt-sources 3.1.33 → 3.1.34

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1bc10d05cb25aa6e8c21a838af30f8e910915411
-  data.tar.gz: 5c1443c4088a393a33513884813ef3eb9b276ff7
+  metadata.gz: 222e00304bac396cf21d2c16d3b3d73b76749d69
+  data.tar.gz: 2eb84c4bb74c787554035622c10580979caba9a0
 SHA512:
-  metadata.gz: 9c2c009324e163840751e84ec0b2eeaff7ed02588637140f26563814183ef43666c2118b92c560cf5fff56c30d9913160e0a940092b4327259f1b18d66efa7fd
-  data.tar.gz: dc09879abc9d3b1f60ff9ecc68f4a2d34da8dfbc19aa6cfcc5640d773d8412b8aa5e3a630dba0b8a8f54c1753dfd88d61c5b50bec8a94694798e0ab376a5804d
+  metadata.gz: e9e2c189ebf74412d2a79d8ec24aff2083d231f6dbba5a3769b4f4d4b6aed70c2553fc3be31fe24ac5ec536fd238a430f451e6379da9584f946952b3505de1d0
+  data.tar.gz: 64cc94c0c8754622afb9af86e5d1ed281a35f46a5f0085fbaeded87ef22dc2a66a7d4a4bad6f20f3a6804f6f4ce00048e58fda69816da353abefd9ecbf9d925f

data/lib/rbbt/sources/cancer_genome_interpreter.rb

@@ -0,0 +1,73 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+require 'rbbt/sources/organism'
+
+module CancerGenomeInterpreter
+  extend Resource
+  self.subdir = 'share/databases/CancerGenomeInterpreter'
+
+  def self.organism(org="Hsa")
+    Organism.default_code(org)
+  end
+
+  #self.search_paths = {}
+  #self.search_paths[:default] = :lib
+
+
+  CancerGenomeInterpreter.claim CancerGenomeInterpreter['.source']["catalog_of_cancer_genes_latest.zip"], :url, "https://www.cancergenomeinterpreter.org/data/catalog_of_cancer_genes_latest.zip"
+
+  CancerGenomeInterpreter.claim CancerGenomeInterpreter.mode_of_action, :proc do 
+    TmpFile.with_file do |tmpdir|
+      Open.mkdir tmpdir
+      Misc.in_dir tmpdir do 
+        `unzip '#{CancerGenomeInterpreter['.source']["catalog_of_cancer_genes_latest.zip"].produce.find}'`
+        tsv = TSV.open('gene_MoA.tsv', :header_hash => '', :type => :single)
+        tsv.key_field = "Associated Gene Name"
+        tsv.namespace = CancerGenomeInterpreter.organism
+        tsv.fields = ["Mode of Action"]
+        tsv
+      end
+    end
+  end
+
+  CancerGenomeInterpreter.claim CancerGenomeInterpreter.mutation_and_CNA, :proc do 
+    TmpFile.with_file do |tmpdir|
+      Open.mkdir tmpdir
+      Misc.in_dir tmpdir do 
+        `unzip '#{CancerGenomeInterpreter['.source']["catalog_of_cancer_genes_latest.zip"].produce.find}'`
+        tsv = TSV.open('cancer_genes_upon_mutations_or_CNAs.tsv', :header_hash => '', :type => :list)
+        tsv.key_field = "Associated Gene Name"
+        tsv.namespace = CancerGenomeInterpreter.organism
+        tsv
+      end
+    end
+  end
+
+  CancerGenomeInterpreter.claim CancerGenomeInterpreter.translocations, :proc do 
+    TmpFile.with_file do |tmpdir|
+      Open.mkdir tmpdir
+      Misc.in_dir tmpdir do 
+        `unzip '#{CancerGenomeInterpreter['.source']["catalog_of_cancer_genes_latest.zip"].produce.find}'`
+        tsv = TSV.open('cancer_genes_upon_trans.tsv', :header_hash => '', :type => :list)
+        tsv.namespace = CancerGenomeInterpreter.organism
+        tsv
+      end
+    end
+  end
+  
+  CancerGenomeInterpreter.claim CancerGenomeInterpreter.acronyms, :proc do 
+    TmpFile.with_file do |tmpdir|
+      Open.mkdir tmpdir
+      Misc.in_dir tmpdir do 
+        `unzip '#{CancerGenomeInterpreter['.source']["catalog_of_cancer_genes_latest.zip"].produce.find}'`
+        TSV.open('cancer_acronyms.tsv', :header_hash => '', :type => :single)
+      end
+    end
+  end
+end
+
+iif CancerGenomeInterpreter.mode_of_action.produce.find if __FILE__ == $0
+iif CancerGenomeInterpreter.mutation_and_CNA.produce.find if __FILE__ == $0
+iif CancerGenomeInterpreter.translocations.produce.find if __FILE__ == $0
+iif CancerGenomeInterpreter.acronyms.produce.find if __FILE__ == $0
+

data/lib/rbbt/sources/intogen.rb

@@ -0,0 +1,48 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+
+module Intogen
+  extend Resource
+  self.subdir = 'share/databases/Intogen'
+
+  #def self.organism(org="Hsa")
+  #  Organism.default_code(org)
+  #end
+
+  #self.search_paths = {}
+  #self.search_paths[:default] = :lib
+
+
+  Intogen.claim Intogen['.source']["intogen_driver_mutations_catalog.zip"], :proc do |filename|
+    raise "Download the fila at 'https://www.intogen.org/downloads?file=/repository/downloads/intogen_driver_mutations_catalog-2016.5.zip' into '#{filename}'"
+  end
+
+  Intogen.claim Intogen.driver_mutations_catalog, :proc do |filaname|
+    all_tsv = nil
+    TmpFile.with_file do |tmpdir|
+      Open.mkdir tmpdir
+      Misc.in_dir tmpdir do 
+        `unzip '#{Intogen['.source']["intogen_driver_mutations_catalog.zip"].produce.find}'`
+        Dir.glob("./*/mutation_analysis.tsv").each do |file|
+          cohort = File.basename(File.dirname(file))
+
+          parser = TSV::Parser.new file, :header_hash => '', :type => :list
+          if all_tsv.nil?
+            all_tsv = TSV.setup({}, :key_field => 'Mutation ID', :fields => ["Sample", "Cohort", "Genomic Mutation"] + parser.fields, :type => :list) 
+          end
+
+          TSV.traverse parser, :into => all_tsv do |sample, values|
+            chr, strand, pos, ref, alt, *rest = values
+            mutation = [chr, pos, alt] * ":"
+            id = [sample, mutation] * "_"
+            [id, [sample, cohort, mutation] + values]
+          end
+        end
+      end
+    end
+    all_tsv.to_s
+  end
+end
+
+iif Intogen.driver_mutations_catalog.produce.find if __FILE__ == $0
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.33
+  version: 3.1.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-20 00:00:00.000000000 Z
+date: 2019-03-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -107,6 +107,7 @@ files:
 - lib/rbbt/sources/barcode.rb
 - lib/rbbt/sources/bibtex.rb
 - lib/rbbt/sources/biomart.rb
+- lib/rbbt/sources/cancer_genome_interpreter.rb
 - lib/rbbt/sources/cath.rb
 - lib/rbbt/sources/clinvar.rb
 - lib/rbbt/sources/corum.rb
@@ -115,6 +116,7 @@ files:
 - lib/rbbt/sources/entrez.rb
 - lib/rbbt/sources/go.rb
 - lib/rbbt/sources/gscholar.rb
+- lib/rbbt/sources/intogen.rb
 - lib/rbbt/sources/jochem.rb
 - lib/rbbt/sources/kegg.rb
 - lib/rbbt/sources/matador.rb