rbbt-sources 3.1.21 → 3.1.22

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2bdca7fd8c0c9f60055453c7f318a699eae54738
-  data.tar.gz: c0b08856ddd9668b6dbbadd2035653ce24506f04
+  metadata.gz: 6ea2d8738ff8b0d863b3bf5ba98033c4ba1c7fe0
+  data.tar.gz: 3a530a18c08891019bc107d2e28b138eafd1e92b
 SHA512:
-  metadata.gz: 4e515516855aa249e758a23da1d1d16915697cf3647bf88c0791b5593b435c2adf4b44006081473d4068a76b55d8b018093cba49070144044c68aa3d9611450c
-  data.tar.gz: eed95d673673f5ec047b37911c44d6876fbd55d7efdc4884863902f6d76bdeda22e5ac5a1982344488ff8fb68808c8233df78eb0baa1e9fa5a2d712485296577
+  metadata.gz: b0268721e94bd69fd1723049d47f041f4be13a6b860bb612c75344d4e56ada4886fba64cba7a63c81a8058b7245acb59ee8abd9d75024fd1437269cbe256cf14
+  data.tar.gz: 0e531a35db84e9151a02197585740ba44792e9ddc3b12586eb790c6eaa2aa48dfc74624e199f4b5c6de97860bc08057f9915aad5041fbdb1920e78f5d9d3fa2b

data/lib/rbbt/sources/PRO.rb

@@ -0,0 +1,47 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+
+module PRO
+  extend Resource
+  self.subdir = 'share/databases/PRO'
+
+  def self.organism(org="Hsa")
+    require 'rbbt/sources/organism'
+    Organism.default_code(org)
+  end
+
+  #self.search_paths = {}
+  #self.search_paths[:default] = :lib
+
+  PRO.claim PRO.identifiers, :proc do 
+    url = "ftp://ftp.pir.georgetown.edu/databases/ontology/pro_obo/PRO_mappings/uniprotmapping.txt"
+
+    dumper = TSV::Dumper.new :key_field => "PRO ID", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :namespace => PRO.organism
+    dumper.init
+    TSV.traverse Open.open(url), :type => :array, :into => dumper, :bar => true do |line|
+      pro, uni = line.split("\t")
+      [pro, [uni.split(":").last]]
+    end
+  end
+
+  PRO.claim PRO.uniprot_equivalences, :proc do
+    
+    dumper = TSV::Dumper.new :key_field => "UniProt/SwissProt Accession", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :namespace => PRO.organism
+    dumper.init
+    TSV.traverse PRO.identifiers, :into => dumper, :bar => true do |pro,values|
+      res = []
+      res.extend MultipleResult
+      unis = values.first
+
+      unis.each do |uni|
+        res << [uni,unis]
+      end
+
+      res
+    end
+  end
+end
+
+iif PRO.identifiers.produce.find if __FILE__ == $0
+iif PRO.uniprot_equivalences.produce(true).find if __FILE__ == $0
+

data/lib/rbbt/sources/go.rb

@@ -6,9 +6,17 @@ require 'rbbt/persist/tsv'
 # now all it does is provide a translation form id to the actual names.
 module GO
 
+  extend Resource
+  
+  extend Resource
+  self.subdir = 'share/databases/GO'
+
   #Rbbt.claim Rbbt.share.databases.GO.gslim_generic, :url, 'http://www.geneontology.org/GO_slims/goslim_generic.obo'
-  Rbbt.claim Rbbt.share.databases.GO.gene_ontology, :url, 'http://purl.obolibrary.org/obo/go.obo'
-  Rbbt.claim Rbbt.share.databases.GO.annotations, :url, 'http://geneontology.org/gene-associations/goa_human.gaf.gz'
+  GO.claim GO.gene_ontology, :url, 'http://purl.obolibrary.org/obo/go.obo'
+  GO.claim GO.Hsa.annotations, :url, 'http://geneontology.org/gene-associations/goa_human.gaf.gz'
+
+  GO.claim GO.annotations, :url, 'http://geneontology.org/gene-associations/goa_human.gaf.gz'
+
 
   MULTIPLE_VALUE_FIELDS = %w(is_a)
   TSV_GENE_ONTOLOGY = File.join(Persist.cachedir, 'gene_ontology')

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.21
+  version: 3.1.22
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-01 00:00:00.000000000 Z
+date: 2017-12-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -97,6 +97,7 @@ files:
 - lib/rbbt/sources/MCLP.rb
 - lib/rbbt/sources/MSigDB.rb
 - lib/rbbt/sources/NCI.rb
+- lib/rbbt/sources/PRO.rb
 - lib/rbbt/sources/PSI_MI.rb
 - lib/rbbt/sources/STITCH.rb
 - lib/rbbt/sources/barcode.rb