rbbt-sources 3.1.22 → 3.1.23

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6ea2d8738ff8b0d863b3bf5ba98033c4ba1c7fe0
-  data.tar.gz: 3a530a18c08891019bc107d2e28b138eafd1e92b
+  metadata.gz: 7e56141cb916b51e2204fac0392eff2d6cd365d1
+  data.tar.gz: 9cc540da01980356fdef07b24158f9cc6eb1640b
 SHA512:
-  metadata.gz: b0268721e94bd69fd1723049d47f041f4be13a6b860bb612c75344d4e56ada4886fba64cba7a63c81a8058b7245acb59ee8abd9d75024fd1437269cbe256cf14
-  data.tar.gz: 0e531a35db84e9151a02197585740ba44792e9ddc3b12586eb790c6eaa2aa48dfc74624e199f4b5c6de97860bc08057f9915aad5041fbdb1920e78f5d9d3fa2b
+  metadata.gz: d858ee55af7164f64ae8a4c60519edc242a5f26b08892138df7732c02d0acca887ac4eeda20da62e320718e98dba18457d1be1d821096a66344d33376964486d
+  data.tar.gz: c14fb8321b65bfdf1aa93bc490032c84f2d9fb92d98b5d77e816e651fbca4181490292e17e6ba8c6b78c71814707a2aa1a25ff51d97470da5f3fad589386af98

data/lib/rbbt/sources/signor.rb

@@ -1,5 +1,6 @@
 require 'rbbt-util'
 require 'rbbt/resource'
+require 'rbbt/sources/uniprot'
 
 module Signor
   extend Resource
@@ -63,7 +64,8 @@ module Signor
     require 'rbbt/sources/organism'
 
     organism = Organism.default_code("Hsa")
-    uni2name = Organism.identifiers(organism).index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
+    #uni2name = Organism.identifiers(organism).index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
+    uni2name = UniProt.identifiers.Hsa.index :target => "Associated Gene Name", :fields => ["UniProt/SwissProt Accession"], :persist => true
 
     parser = TSV::Parser.new Signor.data
     fields = parser.fields

data/lib/rbbt/sources/uniprot.rb

@@ -9,6 +9,62 @@ module UniProt
   extend Resource
   self.subdir = "share/databases/UniProt"
 
+  def self.get_organism_ids(url, organism = nil)
+    tsv = {}
+    fields = []
+    TSV.traverse url, :type => :array, :bar => "Extracting UniProt IDs #{organism}" do |line|
+      uni, type, value = line.split("\t")
+      fields << type unless fields.include?(type)
+      pos = fields.index type
+
+      values = tsv[uni] 
+      values = [] if values.nil?
+      values[pos] ||= []
+      values[pos] << value
+      tsv[uni] = values
+    end
+    fields =  fields.collect do |field|
+      case field
+      when "Gene_Name"
+        "Associated Gene Name"
+      when "Ensembl"
+        "Ensembl Gene ID"
+      when "Ensembl_TRS"
+        "Ensembl Transcript ID"
+      when "Ensembl_PRO"
+        "Ensembl Protein ID"
+      else
+        field
+      end
+    end
+
+    new = TSV.setup({}, :key_field => "UniProt/SwissProt Accession", :fields => fields, :type => :double, :namespace => organism)
+    num_fields = fields.length
+    tsv.each do |k,values|
+      new_values = [nil] * num_fields
+      new_values = values
+      num_fields.times do |i|
+        new_values[i] = [] if new_values[i].nil?
+      end
+      new[k] = new_values
+    end
+    Log.tsv new
+    new
+  end
+
+  UniProt.claim UniProt.identifiers.Hsa, :proc do
+    url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz"
+    tsv = UniProt.get_organism_ids(url, "Hsa")
+    tsv.to_s
+  end
+
+  UniProt.claim UniProt.identifiers.Mmu, :proc do
+    url = "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/MOUSE_10090_idmapping.dat.gz"
+    tsv = UniProt.get_organism_ids(url, "Mmu")
+    tsv.to_a
+  end
+
+
   UniProt.claim UniProt.annotated_variants, :proc do
     url = "http://www.uniprot.org/docs/humsavar.txt"
     tsv = TSV.open(CMD.cmd('tail -n +31 | head -n -4|grep "[[:alpha:]]"', :in => Open.open(url), :pipe => true), 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.22
+  version: 3.1.23
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-05 00:00:00.000000000 Z
+date: 2017-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util