rbbt-sources 3.1.8 → 3.1.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c036392b978d10961a6834bbcb520f90f685dad5
-  data.tar.gz: 1c3104e16b49cf2445a7587fd4e47eb9add3ec54
+  metadata.gz: 4de6a2e2ce1b66916e6bfc8f0e336eca6b55e6a6
+  data.tar.gz: 5cae8b56631ed29ef195f22fc36c73015dce86eb
 SHA512:
-  metadata.gz: 4f5d81a9595cb6f58856e51dbe908862105d268ee64af901aae7e56c0ac5d58bdd34a9780efcb57ca3fa2dcbff352b4e2f5ec62ef6bd662fb747beb726ff64e2
-  data.tar.gz: 005bb8687b44426316d3d758401da95e236b6abddb6d09362ef5706a8f5dc9fa53a4e5f5a2eed29cc7987ae16cba04ce88fe664d4b43a392e6c4cbf642c93c89
+  metadata.gz: c99d530f44054a5e2ddbb8dde13f182c1581172f73455051115045debb1efb140be2d42cb3c40e6156bfaf44bb3dc91c59d05af64967485031d9b81360a5e412
+  data.tar.gz: e4a3100bb65cbb65ca6ca7dec42c5f666b500157891a130cf34d86310aa544feac3739aae05efc347c47abf2195d05cf9d801dc218efe758066517f33e06ffec

data/lib/rbbt/sources/corum.rb

@@ -1,5 +1,6 @@
 require 'rbbt-util'
 require 'rbbt/resource'
+require 'rbbt/sources/organism'
 
 module CORUM
   extend Resource
@@ -10,17 +11,19 @@ module CORUM
   end
 
   CORUM.claim CORUM.complex_names, :proc do 
-    url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
-    tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
+    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
+    tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
     tsv.namespace = organism
     tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
     tsv.key_field = "CORUM Complex ID"
-    tsv.slice("Complex name").to_single
+    tsv = tsv.slice("ComplexName").to_single
+    tsv.fields = ["Complex name"]
+    tsv
   end
 
   CORUM.claim CORUM.complexes, :proc do 
-    url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
-    tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
+    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
+    tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
     tsv.namespace = organism
     tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}.collect{|f|
       case f

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.8
+  version: 3.1.9
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-07 00:00:00.000000000 Z
+date: 2017-01-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -175,7 +175,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.6
+rubygems_version: 2.6.6
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)