crb-blast 0.6.5 → 0.6.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: c6e549532d5ab7c3e2320affbd7b9db0e01dc741
-  data.tar.gz: 7c2a58f1f51381c673bf8906f6e12739b58a7cab
+  metadata.gz: 275e3d2996f91648e9f046cd7a08c4c663243765
+  data.tar.gz: 4de455ec18f7c657585326d94e43dc761403cf77
 SHA512:
-  metadata.gz: 236fb67036142084a61df53041428fe7e6b96abb3ffcced4ed27f86de32d26f6a68a0165ea2052b26bdc96ed7f882b2e791ee45b228dce01b9f8a33f1b80f322
-  data.tar.gz: 02b62ece6ae514db40cd53a94e369c6653213420ae14a7249bc34dd4e1e92e02767d46cabbc588020969d82927203dd3cb5a2e40af37a2f6029f4eec6940dd21
+  metadata.gz: b2725a63477308471676fbdabfd035fc83a469adede3ce56d49bd9020bf779ad53f6f3edec65e6ea744666dbe1df879116248f6ecfa8bdfa86dfdd4b393c2ca4
+  data.tar.gz: 6a731db6a14a8b8c24394891fe3335082e5b664e44314d18324f1072e76a78f37ec3152e459dc0500b293e836958bb84a6e9733961a77fb87a4cda16ee043d56

data/Rakefile

@@ -4,5 +4,23 @@ Rake::TestTask.new do |t|
   t.libs << 'test'
 end
 
+Rake::TestTask.new do |t|
+  t.name = :one
+  t.libs << 'test'
+  t.test_files = ['test/test_test.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :two
+  t.libs << 'test'
+  t.test_files = ['test/test_test2.rb']
+end
+
+Rake::TestTask.new do |t|
+  t.name = :three
+  t.libs << 'test'
+  t.test_files = ['test/test_test3.rb']
+end
+
 desc "Run tests"
 task :default => :test

data/lib/crb-blast/hit.rb

@@ -8,8 +8,8 @@ module CRB_Blast
 
     def initialize(list, qprot, tprot)
       raise(RuntimeError, "unexpected number of columns") if list.length < 14
-      @query      = list[0].split(/[\|\ ]/).first
-      @target     = list[1].split(/[\|\ ]/).first
+      @query      = Bio::FastaDefline.new(list[0]).entry_id
+      @target     = Bio::FastaDefline.new(list[1]).entry_id
       @id         = list[2]
       @alnlen     = list[3].to_i
       @mismatches = list[4].to_i
@@ -33,4 +33,4 @@ module CRB_Blast
     end
   end
 
-end
+end

data/lib/crb-blast/version.rb

@@ -3,7 +3,7 @@ module CRB_Blast
   module VERSION
     MAJOR = 0
     MINOR = 6
-    PATCH = 5
+    PATCH = 6
     BUILD = nil
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')

data/test/query3.fasta

@@ -0,0 +1,65 @@
+>tr|C3Y8C9|C3Y8C9_BRAFL
+ATGGCTGCTGCTGTTTCTACTGTTGGAGCTATTAATAGAGCTCCTCTTTCTCTTAATGGA
+TCTGGATCTGGAGCTGTTTCTGCTCCTGCTTCTACTTTTCTTGGAAAGAAGGTTGTTACT
+GTTTCTAGATTTGCTCAATCTAATAAGAAGTCTAATGGATCTTTTAAGGTTCTTGCTGTT
+AAGGAAGATAAGCAAACTGATGGAGATAGATGGAGAGGACTTGCTTATGATACTTCTGAT
+GATCAACAAGATATTACTAGAGGAAAGGGAATGGTTGATTCTGTTTTTCAAGCTCCTATG
+GGAACTGGAACTCATCATGCTGTTCTTTCTTCTTATGAATATGTTTCTCAAGGACTTAGA
+CAATATAATCTTGATAATATGATGGATGGATTTTATATTGCTCCTGCTTTTATGGATAAG
+CTTGTTGTTCATATTACTAAGAATTTTCTTACTCTTCCTAATATTAAGGTTCCTCTTATT
+CTTGGAATTTGGGGAGGAAAGGGACAAGGAAAGTCTTTTCAATGTGAACTTGTTATGGCT
+AAGATGGGAATTAATCCTATTATGATGTCTGCTGGAGAACTTGAATCTGGAAATGCTGGA
+GAACCTGCTAAGCTTATTAGACAAAGATATAGAGAAGCTGCTGATCTTATTAAGAAGGGA
+AAGATGTGTTGTCTTTTTATTAATGATCTTGATGCTGGAGCTGGAAGAATGGGAGGAACT
+ACTCAATATACTGTTAATAATCAAATGGTTAATGCTACTCTTATGAATATTGCTGATAAT
+CCTACTAATGTTCAACTTCCTGGAATGTATAATAAGGAAGAAAATGCTAGAGTTCCTATT
+ATTTGTACTGGAAATGATTTTTCTACTCTTTATGCTCCTCTTATTAGAGATGGAAGAATG
+GAAAAGTTTTATTGGGCTCCTACTAGAGAAGATAGAATTGGAGTTTGTAAGGGAATTTTT
+AGAACTGATAAGATTAAGGATGAAGATATTGTTACTCTTGTTGATCAATTTCCTGGACAA
+TCTATTGATTTTTTTGGAGCTCTTAGAGCTAGAGTTTATGATGATGAAGTTAGAAAGTTT
+GTTGAATCTCTTGGAGTTGAAAAGATTGGAAAGAGACTTGTTAATTCTAGAGAAGGACCT
+CCTGTTTTTGAACAACCTGAAATGACTTATGAAAAGCTTATGGAATATGGAAATATGCTT
+GTTATGGAACAAGAAAATGTTAAGAGAGTTCAACTTGCTGAAACTTATCTTTCTCAAGCT
+GCTCTTGGAGATGCTAATGCTGATGCTATTGGAAGAGGAACTTTTTATGGAAAGGGAGCT
+CAACAAGTTAATCTTCCTGTTCCTGAAGGATGTACTGATCCTGTTGCTGAAAATTTTGAT
+CCTACTGCTAGATCTGATGATGGAACTTGTGTTTATAATTTT
+>sp|O47426|ATP6_BRAFL
+ATGGCTGGAACTGGACTTTTTGCTGAAATTCTTGATGGAGAAGTTTATAAGTATTATGCT
+GATGGAGAATGGAAGACTTCTTCTTCTGGAAAGTCTGTTGCTATTATGAATCCTGCTACT
+AGAAAGACTCAATATAAGGTTCAAGCTTGTACTCAAGAAGAAGTTAATGCTGTTATGGAA
+CTTGCTAAGTCTGCTCAAAAGTCTTGGGCTAAGACTCCTCTTTGGAAGAGAGCTGAACTT
+CTTCATAAGGCTGCTGCTATTCTTAAGGATAATAAGGCTCCTATGGCTGAATCTCTTGTT
+AAGGAAATTGCTAAGCCTGCTAAGGATTCTGTTACTGAAGTTGTTAGATCTGGAGATCTT
+ATTTCTTATTGTGCTGAAGAAGGAGTTAGAATTCTTGGAGAAGGAAAGTTTCTTCTTTCT
+GATTCTTTTCCTGGAAATGATAGAACTAAGTATTGTCTTACTTCTAAGATTCCTCTTGGA
+GTTGTTCTTGCTATTCCTCCTTTTAATTATCCTGTTAATCTTGCTGTTTCTAAGATTGCT
+CCTGCTCTTATTGCTGGAAATTCTCTTGTTCTTAAGCCTCCTACTCAAGGAGCTGTTTCT
+TGTCTTCATATGGTTCATTGTTTTCATCTTGCTGGATTTCCTAAGGGACTTATTTCTTGT
+ATTACTGGAAAGGGATCTGAAATTGGAGATTTTCTTACTATGCATCCTGCTGTTAATTGT
+ATTTCTTTTACTGGAGGAGATACTGGAATTTCTATTTCTAAGAAGGCTGGAATGATTCCT
+CTTCAAATGGAACTTGGAGGAAAGGATGCTTGTATTGTTCTTGATGATGCTGATCTTGAT
+CTTGTTGCTTCTAATATTATTAAGGGAGGATTTTCTTATTCTGGACAAAGATGTACTGCT
+GTTAAGGTTGTTCTTGTTATGGAATCTGTTGCTGATGAACTTGTTGAAAAGGTTAAGGCT
+AAGGTTGCTAAGCTTACTGTTGGACCTCCTGAAGAAAATTCTGATATTACTGCTGTTGTT
+TCTGAATCTTCTGCTAATTTTATTGAAGGACTTGTTATGGATGCTAAGGAAAAGGGAGCT
+ACTTTTTGTCAAGAATATAAGAGAGAAGGAAATCTTATTTGGCCTCTTCTTCTTGATAAT
+GTTAGACCTGATATGAGAATTGCTTGGGAAGAACCTTTTGGACCTGTTGTTCCTGTTCTT
+AGAATTAATTCTGTTGAAGAAGGAATTAATCATTGTAATGCTTCTAATTTTGGACTTCAA
+GGATGTGTTTTTACTAAGGATATTAATAAGGCTATTCTTATTTCTGATGCTATGGAAACT
+GGAACTGTTCAAATTAATTCTGCTCCTGCTAGAGGACCTGATCATTTTCCTTTTCAAGGA
+CTTAAGGATTCTGGAATTGGATCTCAAGGAGTTACTAATTCTATTAATCTTATGACTAAG
+GTTAAGACTACTGTTATTAATCTTCCTACTCCTTCTTATTCTATGGGAGATGGATTTATT
+TCTAGACTT
+>sp|C4A0D9|BAP1_BRAFL
+ATGGTTATTCTTTCTAATGTTTCTCTTTTTTCTTGTTGTAATATTTCTCAAAAGCCTTCT
+CTTTTTTCTCCTTCTTCTAGATCTTCTCATTGTCCTATTAGATGTTCTCAATCTCAAGAA
+GGAAAGGAAGTTGTTACTTCTCCTCTTAGATCTGTTGTTTGGTCTCTTGGAGAAGAAGTT
+TCTAAGAGATCTCTTTTTGCTCTTGTTTCTGCTTCTCTTTTTTTTGTTGATCCTGCTCTT
+GCTTTTAAGGGAGGAGGACCTTATGGACAAGGAGTTACTAGAGGACAAGATCTTTCTGGA
+AAGGATTTTTCTGGACAAACTCTTATTAGACAAGATTTTAAGACTTCTATTCTTAGACAA
+GCTAATTTTAAGGGAGCTAAGCTTCTTGGAGCTTCTTTTTTTGATGCTGATCTTACTGGA
+GCTGATCTTTCTGAAGCTGATCTTAGAGGAGCTGATTTTTCTCTTGCTAATGTTACTAAG
+GTTAATCTTACTAATGCTAATCTTGAAGGAGCTACTGTTACTGGAAATACTTCTTTTAAG
+GGATCTAATATTACTGGAGCTGATTTTACTGATGTTCCTCTTAGAGATGATCAAAGAGTT
+TATCTTTGTAAGGTTGCTGATGGAGTTAATGCTACTACTGGAAATGCTACTAGAGATACT
+CTTCTTTGTAAT

data/test/test_test.rb

@@ -28,14 +28,6 @@ class TestCRBBlast < Test::Unit::TestCase
       end
     end
 
-    should 'raise error when files don\'t exist' do
-      query = File.join(File.dirname(__FILE__), 'not_query.fasta')
-      target = File.join(File.dirname(__FILE__), 'not_target.fasta')
-      assert_raise IOError do
-        blaster = CRB_Blast::CRB_Blast.new(query, target)
-      end
-    end
-
     should 'setup should run ok' do
       ans = @blaster != nil
       assert_equal ans, true
@@ -85,15 +77,10 @@ class TestCRBBlast < Test::Unit::TestCase
       assert_equal a["scaffold5"][0].target, "AT5G13650.2"
     end
 
-    should 'run' do
-      blaster = CRB_Blast::CRB_Blast.new('test/query.fasta',
-                                         'test/target.fasta')
-      blaster.run 1, 1, false
-      assert blaster.reciprocals
-    end
 
     should 'get number of reciprocals' do
       assert_equal 11, @blaster.size
     end
+
   end
 end

data/test/test_test2.rb

@@ -86,5 +86,6 @@ class Test2CRBBlast < Test::Unit::TestCase
       end
       assert_equal count,70
     end
+
   end
 end

data/test/test_test3.rb

@@ -0,0 +1,55 @@
+#!/usr/bin/env	ruby
+
+require 'helper'
+
+class Test3CRBBlast < Test::Unit::TestCase
+
+  context 'crb-blast' do
+
+    setup do
+
+    end
+
+    teardown do
+      extensions  = ["blast", "nsq", "nin", "nhr", "psq", "pin", "phr"]
+      Dir["*"].each do |file|
+        extensions.each do |extension|
+          if file =~ /.*\.#{extension}$/
+            File.delete(file)
+          end
+        end
+      end
+    end
+
+    should 'raise error when files don\'t exist' do
+      query = File.join(File.dirname(__FILE__), 'not_query.fasta')
+      target = File.join(File.dirname(__FILE__), 'not_target.fasta')
+      assert_raise IOError do
+        blaster = CRB_Blast::CRB_Blast.new(query, target)
+      end
+    end
+
+    should 'run' do
+      blaster = CRB_Blast::CRB_Blast.new('test/query.fasta',
+                                         'test/target.fasta')
+      blaster.run 1, 1, false
+      assert blaster.reciprocals
+    end
+
+    should 'work for query sequences with pipes' do
+      query = File.join(File.dirname(__FILE__), 'query3.fasta')
+      target = File.join(File.dirname(__FILE__), 'target.fasta')
+
+      blaster = CRB_Blast::CRB_Blast.new(query, target)
+      dbs = blaster.makedb
+      run = blaster.run_blast(1e-5, 6, false)
+      load = blaster.load_outputs
+      recip_count = blaster.find_reciprocals
+      recips = blaster.reciprocals
+      assert_equal 3, recip_count, "reciprocal hits"
+      assert recips.has_key?("tr|C3Y8C9|C3Y8C9_BRAFL")
+      assert recips.has_key?("sp|O47426|ATP6_BRAFL")
+      assert recips.has_key?("sp|C4A0D9|BAP1_BRAFL")
+    end
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: 0.6.5
+  version: 0.6.6
 platform: ruby
 authors:
 - Chris Boursnell
@@ -222,11 +222,13 @@ files:
 - test/helper.rb
 - test/query.fasta
 - test/query2.fasta
+- test/query3.fasta
 - test/target.fasta
 - test/target2.fasta
 - test/test_bin.rb
 - test/test_test.rb
 - test/test_test2.rb
+- test/test_test3.rb
 homepage: https://github.com/cboursnell/crb-blast
 licenses:
 - MIT