rbbt-sources 3.1.34 → 3.1.35

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 222e00304bac396cf21d2c16d3b3d73b76749d69
-  data.tar.gz: 2eb84c4bb74c787554035622c10580979caba9a0
+  metadata.gz: ff1cc882305d8bc0a5e81407d78870177f500537
+  data.tar.gz: 260dcaa7cb7e84de2aaf0293027fecb59712c2ba
 SHA512:
-  metadata.gz: e9e2c189ebf74412d2a79d8ec24aff2083d231f6dbba5a3769b4f4d4b6aed70c2553fc3be31fe24ac5ec536fd238a430f451e6379da9584f946952b3505de1d0
-  data.tar.gz: 64cc94c0c8754622afb9af86e5d1ed281a35f46a5f0085fbaeded87ef22dc2a66a7d4a4bad6f20f3a6804f6f4ce00048e58fda69816da353abefd9ecbf9d925f
+  metadata.gz: e63dd46454833e824492e6116b732df01166d87a89d49536d15bda6ce9bf826ef5712ed1a04a3f673a4aad1fc233089071c074fcd3cbbca5fafcf99c08c5f7e7
+  data.tar.gz: c57c92936d4a2afce719d488ad1d5a8e800c13e1d64e01085ca2835f288a2d208ca2e2cbc8badf432b338e38b8fdc8f25dc9b2d1d700a944a21b187950cc3bfd

data/lib/rbbt/sources/organism.rb

@@ -8,6 +8,7 @@ module Organism
 
   ARCHIVE_MONTH_INDEX = {}
   %w(jan feb mar apr may jun jul aug sep oct nov dec).each_with_index{|d,i| ARCHIVE_MONTH_INDEX[d] = i }
+
   def self.compare_archives(a1, a2)
     a1 = a1.partition("/").last if a1 and a1.include? "/"
     a2 = a2.partition("/").last if a2 and a2.include? "/"
@@ -65,21 +66,26 @@ module Organism
 
   def self.hg_build(organism)
     require 'rbbt/sources/ensembl_ftp'
+    return 'hg19' unless organism =~ /\//
 
-    raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
+    species, date = organism.split("/")
 
-    return 'hg20' unless organism =~ /\//
-    date = organism.split("/")[1] 
+    case species
+    when "Hsa"
+      date = organism.split("/")[1] 
 
-    release = Ensembl.releases[date]
+      release = Ensembl.releases[date]
 
-    release_number = release.sub(/.*-/,'').to_i
-    if release_number <= 54 
-      'hg18'
-    elsif release_number <= 75
-      'hg19'
+      release_number = release.sub(/.*-/,'').to_i
+      if release_number <= 54 
+        'hg18'
+      elsif release_number <= 75
+        'hg19'
+      else
+        'hg38'
+      end
     else
-      'hg38'
+      raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
     end
   end
 

data/share/Ensembl/release_dates

@@ -1,5 +1,11 @@
 #: :type=:single
 #Release	build
+release-95	jan2019
+release-94	oct2018
+release-93	jul2018
+release-92	apr2018
+release-91	dec2017
+release-90	aug2017
 release-89	may2017
 release-88	mar2017
 release-87	dec2016

data/share/install/Organism/organism_helpers.rb

@@ -784,3 +784,16 @@ file 'uniprot2ensembl' => ["protein_sequence", "protein_identifiers"] do |t|
   end
   Misc.sensiblewrite(t.name, dumper.stream)
 end
+
+file 'gene_set' do |t|
+  path = File.expand_path(t.name)
+  dirname = File.dirname(path)
+  organism = File.basename(dirname)
+
+  release = Ensembl.org2release(organism)
+  num = release.split("-").last
+  build_code = num.to_i > 75 ? "GRCh38" : "GRCh37" 
+  url = "ftp://ftp.ensembl.org/pub/release-#{num}/gtf/homo_sapiens/Homo_sapiens.#{build_code}.#{num}.gtf.gz"
+  CMD.cmd("wget '#{url}' -O #{t.name}.gz")
+  nil
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.34
+  version: 3.1.35
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-05 00:00:00.000000000 Z
+date: 2019-03-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util