rbbt-sources 3.1.7 → 3.1.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1a2f9d5c13961a7fa8a3c948367f312ad15ae555
-  data.tar.gz: e6ec67742de00219a229d9cc4db6bc4a6fff67fd
+  metadata.gz: c036392b978d10961a6834bbcb520f90f685dad5
+  data.tar.gz: 1c3104e16b49cf2445a7587fd4e47eb9add3ec54
 SHA512:
-  metadata.gz: 0f06fd95e0e4ad122ebbd35bca6cd878de70ee2cc251e99296d055cdbefa055132daf0329f3f2491624e905ac7dad5fb63edada9a88da027639afe2dc8e4e307
-  data.tar.gz: f85b6b37937b24c7a282a0d07c2e567e4db3bb816ef40a12d31f7eaf65bcbe3c1886cad923a73e6732394325161ff7750bf76dba8100aa5db3d91f0224498342
+  metadata.gz: 4f5d81a9595cb6f58856e51dbe908862105d268ee64af901aae7e56c0ac5d58bdd34a9780efcb57ca3fa2dcbff352b4e2f5ec62ef6bd662fb747beb726ff64e2
+  data.tar.gz: 005bb8687b44426316d3d758401da95e236b6abddb6d09362ef5706a8f5dc9fa53a4e5f5a2eed29cc7987ae16cba04ce88fe664d4b43a392e6c4cbf642c93c89

data/etc/allowed_biomart_archives

@@ -4,3 +4,4 @@ jan2013
 feb2014
 dec2013
 dec2014
+dec2015

data/lib/rbbt/sources/pfam.rb

@@ -10,7 +10,7 @@ InterPro.claim InterPro.pfam_names, :proc do
   pfam_domains = Pfam.domains.read.split("\n").collect{|l| l.split("\t").first}.compact.flatten
   tsv = nil
   TmpFile.with_file(pfam_domains * "\n") do |tmpfile|
-    tsv = TSV.open(CMD.cmd("cut -f 4,3 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro.source.protein2ipr.open, :pipe => true), :key_field => 1, :fields => [0], :type => :single)
+    tsv = TSV.open(CMD.cmd("cut -f 4,3 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro[".source"].protein2ipr.open, :pipe => true), :key_field => 1, :fields => [0], :type => :single)
   end
   tsv.key_field = "InterPro ID"
   tsv.fields = ["Domain Name"]
@@ -21,7 +21,7 @@ InterPro.claim InterPro.pfam_equivalences, :proc do
   pfam_domains = Pfam.domains.read.split("\n").collect{|l| l.split("\t").first}.compact.flatten
   tsv = nil
   TmpFile.with_file(pfam_domains * "\n") do |tmpfile|
-    tsv = TSV.open(CMD.cmd("cut -f 2,4 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro.source.protein2ipr.open, :pipe => true), :key_field => 0, :fields => [1], :type => :single)
+    tsv = TSV.open(CMD.cmd("cut -f 2,4 | sort -u |grep -w -f #{ tmpfile }", :in => InterPro[".source"].protein2ipr.open, :pipe => true), :key_field => 0, :fields => [1], :type => :single)
   end
   tsv.key_field = "InterPro ID"
   tsv.fields = ["Pfam Domain"]
@@ -34,7 +34,7 @@ module Pfam
   self.subdir = "share/databases/Pfam"
 
   Pfam.claim Pfam.domains, :proc  do
-    url = "ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
+    url = "ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz"
     tsv = TSV.open(Open.open(url), :key_field => "Pfam Domain ID", :fields => ["Pfam Clan ID", "Code Name", "Name", "Description"])
     tsv.to_s
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.7
+  version: 3.1.8
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-06 00:00:00.000000000 Z
+date: 2016-09-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util