crb-blast 0.4.1 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: e3caa1fa30a20503163a10776ba9800a13068e37
-  data.tar.gz: 5e175e4cb4289a357b2abf22df61453c495c739b
+  metadata.gz: fca3c14697b93c5e9448b78a2ede132d986fd53d
+  data.tar.gz: 943aa5b9c759f3ae2322cba50d161b3d6b11c8d6
 SHA512:
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+  metadata.gz: 7f8311c0fdda302afc7f017a3dc496088c5519e7b58ca19180b7c1fdc7a7032c234bb58489ab02a1034ccb6e0048d7af68740e17028fa17f221affe3879065c3
+  data.tar.gz: b0ab76d52d3dab09625ecf120d0246d1061d31a9b04adb7e1e739ebcf81dc4af5a8d067e6305a260db30ec47c1fd20810b52e965b65135260fdab4a7f1bf1d78

data/bin/crb-blast

@@ -11,7 +11,7 @@ require 'bindeps'
 opts = Trollop::options do
   banner <<-EOS
 
-CRB-Blast v0.3.2 by Chris Boursnell <cmb211@cam.ac.uk>
+CRB-Blast v0.4.2 by Chris Boursnell <cmb211@cam.ac.uk>
 
 Conditional Reciprocal Best BLAST
 

data/crb-blast.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |gem|
   gem.name        = 'crb-blast'
-  gem.version     = '0.4.1'
+  gem.version     = '0.4.2'
   gem.date        = '2014-07-23'
   gem.summary     = "Run conditional reciprocal best blast"
   gem.description = "See summary"

data/lib/crb-blast/crb-blast.rb

@@ -220,6 +220,7 @@ module CRB_Blast
       if !File.exist?(@output1)
         blasts=[]
         files = split_input(@query, threads)
+        threads = [threads, files.length].min
         files.threach(threads) do |thread|
           cmd1 = "#{bin1} -query #{thread} -db #{@working_dir}/#{@target_name} "
           cmd1 << " -out #{thread}.blast -evalue #{evalue} "
@@ -254,6 +255,7 @@ module CRB_Blast
       if !File.exist?(@output2)
         blasts=[]
         files = split_input(@target, threads)
+        threads = [threads, files.length].min
         files.threach(threads) do |thread|
           cmd2 = "#{bin2} -query #{thread} -db #{@working_dir}/#{@query_name} "
           cmd2 << " -out #{thread}.blast -evalue #{evalue} "
@@ -295,8 +297,10 @@ module CRB_Blast
       input = {}
       name = nil
       seq=""
+      sequences=0
       File.open(filename).each_line do |line|
         if line =~ /^>(.*)$/
+          sequences+=1
           if name
             input[name]=seq
             seq=""
@@ -310,6 +314,7 @@ module CRB_Blast
       # construct list of output file handles
       outputs=[]
       output_files=[]
+      pieces = [pieces, sequences].min
       pieces.times do |n|
         outfile = "#{filename}_chunk_#{n}.fasta"
         outfile = File.expand_path(outfile)

data/test/test_test2.rb

@@ -43,6 +43,18 @@ class Test2CRBBlast < Test::Unit::TestCase
       end
     end
 
+    should 'break input file into no more pieces than there are sequences' do
+      files = @blaster.split_input('test/query.fasta', 16)
+      assert_equal 11, files.size
+      files.each do |file|
+        assert File.exist?(file)
+      end
+      # little teardown
+      files.each do |file|
+        File.delete(file)
+      end
+    end
+
     should 'run blast should check if the databases exist yet' do
       tmp = CRB_Blast::CRB_Blast.new('test/query2.fasta',
                                      'test/target2.fasta')

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.2
 platform: ruby
 authors:
 - Chris Boursnell