bio-rocker 0.2.1beta → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 80a163d27ab76ae02864ec1f3b1e288371e8bf50
-  data.tar.gz: c444438d8b9372b6949c900a46dc1dd913efe56b
+  metadata.gz: d1f7834b90614d13e3b1c8f23b56e282b65066aa
+  data.tar.gz: 80cb0cf8a692ee23421167d5d0e7822124fb51f8
 SHA512:
-  metadata.gz: bc9303fd05913c720ca440ad358d3313cd2b601193e4e3bc46d945e4bfef14713f5d2ba1483fa097472e0be44d08f3d426b73d593fd4a4e410f663c2db284c21
-  data.tar.gz: d78afc4fe61106c453a52a87eec977495ac52016af356dc3d60f792da35de16f385c26b9af3df190857529f95d03acbca7edf766e6c439bf4315952506dd9577
+  metadata.gz: 0592a06d98989b18dc7be92243288df57cf01c623e694d3faafd5f800843290b055dba586195a3bac8439d178c9372c77e5a195f47f20fb5142f4e0bae28fc7e
+  data.tar.gz: 88d41e820e038df84995bce99b17551a17181f81e07adf0d1969ff1ece7d53704f25699b44d8748865f00f9dbac77f6c3897b71fec034f04682d1058ed2422c3

data/bin/ROCker

@@ -54,7 +54,7 @@ opts = OptionParser.new do |opt|
       opt.on("-v", "--overlap NUMBER", "Minimum overlap with reference gene to tag a read as positive. By default: '#{ROCker.default :minovl}'."){ |v| o[:minovl]=v.to_f }
       opt.on(      "--genome-frx NUMBER", "Fraction to subsample the positive set genomes to generate the metagenome. By default: #{ROCker.default :genomefrx}"){ |v| o[:genomefrx]=v.to_f }
       opt.on(      "--per-taxon RANK", "If selected, only one genome per taxon is used to build the metagenome. Valid ranks include: species, genus, family, order, class, phylum.",
-	 "This option replaces --per-genus and --per-species, but is temporarily out of service."){ |v| o[:pertaxon]=v.downcase }
+	 "This option replaces --per-genus and --per-species from v0.1.*."){ |v| o[:pertaxon]=v.downcase }
       opt.on(      "--nometagenome", "Do not create metagenome. Implies --noblast. By default, metagenome is created."){ |v| o[:nomg]=v }
       opt.on(      "--noblast", "Do not execute BLAST. By default, BLAST is executed."){ |v| o[:noblast]=v }
       opt.on(      "--noalignment", "Do not align reference set. By default, references are aligned."){ |v| o[:noaln]=v }

data/lib/rocker.rb

@@ -2,7 +2,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update May-07-2015
+# @update May-14-2015
 #
 
 require 'rocker/blasthit'
@@ -18,7 +18,7 @@ class ROCker
       :positive=>[], :negative=>[], :thr=>2,:genomefrx=>1.0,
 	 # ext. software
 	 :grinder=>'grinder', :muscle=>'muscle', :blastbins=>'', :seqdepth=>3, :minovl=>0.75,
-	 :grindercmd=>'%1$s -reference_file "%2$s" -cf "%3$f" -base_name "%4$s" -dc \'-~*Nn\' -md "poly4 3e-3 3.3e-8" -mr "95 5" -rd "100 uniform 5"',
+	 :grindercmd=>'%1$s -reference_file "%2$s" -cf "%3$f" -base_name "%4$s" -dc \'-~*Nn\' -md "uniform 0.1" -mr "95 5" -rd "100 uniform 5"',
 	 :musclecmd=>'%1$s -in "%2$s" -out "%3$s" -quiet',
 	 :blastcmd=>'%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" -num_threads %6$d -outfmt 6 -max_target_seqs 1',
 	 :makedbcmd=>'%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"',
@@ -132,8 +132,10 @@ class ROCker
 	    doc = res.split("\n").grep(/^[^#]/)
 	 end
 	 doc.each do |ln|
+	    next if ln =~ /^#/
 	    r = ln.chomp.split /\t/
-	    prots = r[8].split(/;/).grep(/^db_xref=UniProtKB\/TrEMBL:/){ |xref| xref.split(/:/)[1] }
+	    next if r.size < 9
+	    prots = r[8].split(/;/).grep(/^db_xref=UniProtKB[\/A-Za-z-]*:/){ |xref| xref.split(/:/)[1] }
 	    p = prots.select{ |p| @o[:positive].include? p }.first
 	    next if p.nil?
 	    positive_coords[ r[0] ] ||= []
@@ -148,10 +150,12 @@ class ROCker
       print "\n" unless @o[:q]
       unless @o[:pertaxon].nil?
 	 genome_ids[:positive] = genome_org.values
-	 puts "  Using #{genome_org.size} genomes after filtering by #{@o[:pertaxon]}." unless @o[:q]
+	 puts "  Using #{genome_org.size} genome(s) 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(:+)
+      found = positive_coords.values.map{ |a| a.map{ |b| b[:prot_id] } }.reduce(:+)
+      raise "Cannot find the genomic location of any provided sequence." if found.nil?
+      missing = @o[:positive] - found
       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?
       
       # Download genomes

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 0.2.1beta
+  version: 0.2.4
 platform: ruby
 authors:
 - Luis (Coto) Orellana
@@ -56,9 +56,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>'
+  - - '>='
     - !ruby/object:Gem::Version
-      version: 1.3.1
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.0.14