bio-rocker 0.2.0alpha → 0.2.1beta

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 83c3e3b92659ce86b8bc1c2119b3d37db119b432
-  data.tar.gz: 0f27ba6ed5086baf64e99732dc86a4c7e31432d9
+  metadata.gz: 80a163d27ab76ae02864ec1f3b1e288371e8bf50
+  data.tar.gz: c444438d8b9372b6949c900a46dc1dd913efe56b
 SHA512:
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-  data.tar.gz: c8bda317dda0da8eed23cd976eb6c848f866382e37f5c8315bbd365fe65f85f7319a60eb2c2d511461fca4e329af403c31ccd77a16c0a880ec720edfd9ac269f
+  metadata.gz: bc9303fd05913c720ca440ad358d3313cd2b601193e4e3bc46d945e4bfef14713f5d2ba1483fa097472e0be44d08f3d426b73d593fd4a4e410f663c2db284c21
+  data.tar.gz: d78afc4fe61106c453a52a87eec977495ac52016af356dc3d60f792da35de16f385c26b9af3df190857529f95d03acbca7edf766e6c439bf4315952506dd9577

data/bin/ROCker

@@ -6,7 +6,8 @@
 # @update May-07-2015
 #
 
-$:.push File.expand_path(File.dirname(__FILE__) + '/../lib')
+lib = File.expand_path(File.dirname(__FILE__) + '/../lib')
+$:.push lib if Dir.exists? lib
 require 'rocker'
 require 'optparse'
 

data/lib/rocker.rb

@@ -114,7 +114,11 @@ class ROCker
       i = 0
       genome_ids[:positive].each do |genome_id|
 	 print "  * scanning #{(i+=1).ordinalize} genome out of #{genome_ids[:positive].size}. \r" unless @o[:q]
-	 # ToDo check organism name using genome_org unless @o[:pertaxon].nil?
+	 unless @o[:pertaxon].nil?
+	    genome_taxon = genome2taxon(genome_id, @o[:pertaxon])
+	    next unless genome_org[ genome_taxon ].nil?
+	    genome_org[ genome_taxon ] = genome_id
+	 end
 	 $stderr.puts "   # Looking for any of #{@o[:positive]}" if @o[:debug]
 	 genome_file = @o[:baseout] + '.src.' + i.to_s + '.gff3'
 	 if @o[:reuse] and File.exist? genome_file
@@ -142,7 +146,10 @@ class ROCker
 	 end
       end
       print "\n" unless @o[:q]
-      genome_ids[:positive] = genome_org.values unless @o[:pertaxon].nil?
+      unless @o[:pertaxon].nil?
+	 genome_ids[:positive] = genome_org.values
+	 puts "  Using #{genome_org.size} genomes after filtering by #{@o[:pertaxon]}." unless @o[:q]
+      end
       all_genome_ids = genome_ids.values.reduce(:+).uniq
       missing = @o[:positive] - positive_coords.values.map{ |a| a.map{ |b| b[:prot_id] } }.reduce(:+)
       warn "\nWARNING: Cannot find genomic location of sequence(s) #{missing.join(',')}.\n\n" unless missing.size==0 or @o[:genomefrx]<1.0 or not @o[:pertaxon].nil?
@@ -430,6 +437,15 @@ class ROCker
       end
       genomes.uniq
    end
+   def genome2taxid(genome_id)
+      ln = ebiFetch('embl', [genome_id], 'annot').split(/[\n\r]/).grep(/^FT\s+\/db_xref="taxon:/).first
+      return ln if ln.nil?
+      ln.sub(/.*"taxon:(\d+)".*/, "\\1")
+   end
+   def genome2taxon(genome_id, rank='species')
+      xml = ebiFetch('taxonomy', [genome2taxid(genome_id)], 'enataxonomyxml').gsub(/\s*\n\s*/,'')
+      xml.scan(/<taxon [^>]+>/).grep(/rank="#{rank}"/).first.sub(/.* taxId="(\d+)".*/,"\\1")
+   end
    def restcall(url, outfile=nil)
       response = RestClient.get url
       raise "Unable to reach EBI REST client, error code #{response.code}." unless response.code == 200

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 0.2.0alpha
+  version: 0.2.1beta
 platform: ruby
 authors:
 - Luis (Coto) Orellana