Test phyta-extract

PalMuc · Oct 21, 2011 · 4c5ec2a · 4c5ec2a
1 parent 9e75497
commit 4c5ec2a
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Showing 11 changed files with 215 additions and 10 deletions.
diff --git a/bin/phyta-extract b/bin/phyta-extract
@@ -28,7 +28,7 @@ require 'trollop'
 #parse command line arguments
 opts = Trollop::options do
   opt :fasta, "The file containing the sequences in FASTA format", :type => String
-  opt :input_clean, "The name of the clean sequence table in CSV format", :type => String
+  opt :input_clean, "The name of the clean sequence table in CSV format", :type => String, :short => "-c"
   opt :input_contaminated, "The name of the contaminated sequence table in CSV format", :type => String, :short => "-d"
 
   opt :output_clean, "The name of the FASTA file where clean sequences will be written to", :type => String, :short => "-o"
@@ -47,12 +47,6 @@ rootpath = File.dirname(File.dirname(__FILE__))
 PHYTA_VERSION = File.new(File.join(rootpath,'VERSION')).read.chomp
 puts "Running #{SCRIPT_NAME} #{PHYTA_VERSION}"
 
-opts[:fasta] = ARGV.shift
-opts[:input_clean] = ARGV.shift
-opts[:input_contaminated] = ARGV.shift
-opts[:output_clean] = ARGV.shift
-opts[:output_contaminated] = ARGV.shift
-
 unless File.exists?(opts[:fasta])
   abort "The input file at " + File.expand_path(opts[:fasta]) + " could not be opened!"
 end

diff --git a/test/data/extract/clean_empty_clean.csv b/test/data/extract/clean_empty_clean.csv
diff --git a/test/data/extract/clean_empty_clean_target.fasta b/test/data/extract/clean_empty_clean_target.fasta
diff --git a/test/data/extract/clean_empty_contaminated.csv b/test/data/extract/clean_empty_contaminated.csv
@@ -0,0 +1,2 @@
+query sequence id;hit accession number;sgi;evalue;species;subject annotation;subject score;kingdom
+AW5C4;XP_001629010;156372369;1.85315736381546e-09;Astrosclera willeyana;predicted protein;66.2401644268205;Parabasalia
diff --git a/test/data/extract/clean_empty_contaminated_target.fasta b/test/data/extract/clean_empty_contaminated_target.fasta
@@ -0,0 +1,15 @@
+>AW5C4 [Astrosclera_willeyana]
+CGGCCGGGCAGCACAACTTCTAACGGTGGACCCCTCGGCTCGTGCATCGATGAAGAACGC
+AGCAAACTGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACG
+CAAATGGCGCTCCCGGTCAAGCCGGGAGCACGTCTGTCTGAGCGTCCTTTTCATTGAAGT
+GCAAGCCTTGCGTTTGCAGTGATTTGAGGAGTTGTCGAGTGCCTTTCCGAGTCGCCGGCA
+TCCCTTGAAGTCGTGCACTGTCCGTCACAGACAGCCAAGTGCAGGAGAGTTGCTTGCGCT
+TGGACTTCTGTGCGAGACTTGTGTTGAGAGCCCACTTTTGTACAGTTGgacctcagatca
+ggcgaggctacctgctgaacttaagcatatcaataagcagaggaaaagaaactaacaagg
+attcccccagtaacggcgagcgaagtgggaaaagctcgagcctgaaatctctggcagttg
+atgccagcgaattgtggccgggagaggcagctggaccctggctagcgctgtcgaagttga
+cctggaaaggcacgtcagagagggtgacagccccgtgtgcgacactgccgggcagggcca
+ccactgtcttcagagagtcgggttgtttgggaatgcagcccaaagtgggtggtaaactcc
+atctaaagctaaatatgggcacgagaccgatagcaaacaagtaccgtgagcggaaaaaaa
+aaaaaaaAAAAAAAAAAAAAAANTTGGGGCCCCCCCCCCCCCNNCAATTTTTAATCCAAA
+AAATTTTTTTTTGGGGGCCCCATTTNGGGCCCTTTGGGCAATTTCCCCCTTAAGGGGG
diff --git a/test/data/extract/contaminated_empty_clean.csv b/test/data/extract/contaminated_empty_clean.csv
@@ -0,0 +1,2 @@
+query sequence id;hit accession number;sgi;evalue;species;subject annotation;subject score;kingdom
+AW5C3;XP_001629010;156372369;1.85315736381546e-09;Nota contamination;predicted protein;66.2401644268205;Porifera
diff --git a/test/data/extract/contaminated_empty_clean_target.fasta b/test/data/extract/contaminated_empty_clean_target.fasta
@@ -0,0 +1,11 @@
+>AW5C3 [Astrosclera_willeyana]
+GGGTAATGTTGGGCTTNGATATGGTCAAGCCGGGAAGTTATAAACCAAGCTTTTAAATTA
+ATGTTTNTGGAATAGGANAANNAAAGAGGGCAACAGTCCCGTGAGCGAAAAGAATTTGGC
+TTCCTGAACGTTATTCCCAAGTACTATGGGATAGCCTAAACCTGTAGGAATCTAGGAGGA
+CCACCTCCTAAGGCTAAATATGACTTGGCGACCGTGAAATTGAGTTTGGTGGACCAGGAG
+CAAGATGTCAGAGAAGTTTGGAGACGTTCGTGTCCGTGATGCTGGCCAATATATTGTCAA
+GAACTTTCGCTCATTTCCTCAGTTTGTCGGTCGGTTGATACAGACCTACAGAGCAACATA
+CATCACCTGCAAGACTGTCCGAATGACACCTTACTTCCACATCGTTGGGGTGGCCATCGC
+AATAAACTATATGATTGATTACAAGTACCACTTGAAGTATGAGAAACTGCGCAAATACCA
+CTGAACATTGAACCAAGTTGTACTCACACCTTGTCACATCTGTATAGACACAAAGGTCCA
+TCATATGGTGCTGCATTGTATGCC
diff --git a/test/data/extract/contaminated_empty_contaminated.csv b/test/data/extract/contaminated_empty_contaminated.csv
diff --git a/test/data/extract/contaminated_empty_contaminated_target.fasta b/test/data/extract/contaminated_empty_contaminated_target.fasta
diff --git a/test/data/extract/truncated.fasta b/test/data/extract/truncated.fasta
@@ -0,0 +1,138 @@
+>AW5C4 [Astrosclera_willeyana]
+CGGCCGGGCAGCACAACTTCTAACGGTGGACCCCTCGGCTCGTGCATCGATGAAGAACGC
+AGCAAACTGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACG
+CAAATGGCGCTCCCGGTCAAGCCGGGAGCACGTCTGTCTGAGCGTCCTTTTCATTGAAGT
+GCAAGCCTTGCGTTTGCAGTGATTTGAGGAGTTGTCGAGTGCCTTTCCGAGTCGCCGGCA
+TCCCTTGAAGTCGTGCACTGTCCGTCACAGACAGCCAAGTGCAGGAGAGTTGCTTGCGCT
+TGGACTTCTGTGCGAGACTTGTGTTGAGAGCCCACTTTTGTACAGTTGgacctcagatca
+ggcgaggctacctgctgaacttaagcatatcaataagcagaggaaaagaaactaacaagg
+attcccccagtaacggcgagcgaagtgggaaaagctcgagcctgaaatctctggcagttg
+atgccagcgaattgtggccgggagaggcagctggaccctggctagcgctgtcgaagttga
+cctggaaaggcacgtcagagagggtgacagccccgtgtgcgacactgccgggcagggcca
+ccactgtcttcagagagtcgggttgtttgggaatgcagcccaaagtgggtggtaaactcc
+atctaaagctaaatatgggcacgagaccgatagcaaacaagtaccgtgagcggaaaaaaa
+aaaaaaaAAAAAAAAAAAAAAANTTGGGGCCCCCCCCCCCCCNNCAATTTTTAATCCAAA
+AAATTTTTTTTTGGGGGCCCCATTTNGGGCCCTTTGGGCAATTTCCCCCTTAAGGGGG
+>AW3C1 [Astrosclera_willeyana]
+CGGCCGGGCAGCACAACTTCTAACGGTGGACCCCTCGGCTCGTGCATCGATGAAGAACGC
+AGCAAACTGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACG
+CAAATGGCGCTCCCGGTCAAGCCGGGAGCACGTCTGTCTGAGCGTCCTTTTCATTGAAGT
+GCAAGCCTTGCGTTTGCAGTGATTTGAGGAGTTGTCGAGTGCCTTTCCGAGTCGCCGGCA
+TCCCTTGAAGTCGTGCACTGTCCGTCACAGACAGCCAAGTGCAGGAGAGTTGCTTGCGCT
+TGGACTTCTGTGCGAGACTTGTGTTGAGAGCCCACTTTTGTACAGTTGgacctcagatca
+ggcgaggctacctgctgaacttaagcatatcaataagcagaggaaaagaaactaacaagg
+attcccccagtaacggcgagcgaagtgggaaaagctcgagcctgaaatctctggcagttg
+atgccagcgaattgtggccgggagaggcagctggaccctggctagcgctgtcgaagttga
+cctggaaaggcacgtcagagagggtgacagccccgtgtgcgacactgccgggcagggcca
+ccactgtcttcagagagtcgggttgtttgggaatgcagcccaaagtgggtggtaaactcc
+atctaaagctaaatatgggcacgagaccgatagcaaacaagtaccgtgagcggaaaaaaa
+aaaaaaaAAAAAAAAAAAAAAANTTGGGGCCCCCCCCCCCCCNNCAATTTTTAATCCAAA
+AAATTTTTTTTTGGGGGCCCCATTTNGGGCCCTTTGGGCAATTTCCCCCTTAAGGGGG
+>AW4C1 [Astrosclera_willeyana]
+GGCCGGGGGTTGGTGCTTCAGCTCCNAAAGAAGTGACTTGTGGTGTGAAAGCTCTTGTTT
+GGTGAAGTGTCAGACTCTCCCTCCATCTAGTCAGAATGTGCGACGAGGACGTTGCTGCGT
+TGGTTGTCGACAACGGCTCCGGCATGTGCAAAGCCGGGTTCGCCGGGGATGATGCACCTC
+GCGCTGTGTTCCCTTCCATCGTGGGCCGCCCTCGTCACCAGGGCGTGATGGTGGGTATGG
+GCCAGAAGGACTCGTACGTCGGCGATGAGGCCCAGAGCAAGAGAGGTATCCTCACCCTCA
+AGTACCCCATCGAGCACGGTATCGTTACCAACTGGGACGACATGGAGAAGATCTGGCATC
+ACACCTTCTACAACGAGCTGCGTGTTGCGCCCGAGGAGCACCCCGTTCTCCTAACAGAGG
+CGCCCCTCAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTCGAGACGTTCA
+ATACACCAGCCATGTACGTCGCCATTCAGGCCGTGCTCTCGCTGTACACCTCTGGTCGTA
+CCACCGGTATCGTGTTCGATTCTGGCGACGGAGTCTCCCACACCGTGCCCATCTACGAGG
+GATACGCCCTCCCACACGCCATCCTTCGTCTCGACCTCGCCGGGCGTGATCTGACAGACG
+ACCTGATGAAGATCCTCACCGAGCGTGGCTACTCGTTCACCACAACGGCAGAGCGTGAAA
+TCGTGCGTGACATCAAGGAGAAGCTGTGCTACGTGGCACTAGACTTTGAGCAGGAGATGC
+AAACAGCTGCCTCCAGCTCCAGCATCGAGAAGAGTTATGAGCTTCCTGATGGACAGGTTA
+TCACCATTGGAAACGAGCGCTTTCCGGGCCCCCAAGGCCCTCTTCCGCCCCAGCTTCCGG
+GGAATGGGAGCCGGTGGGATCCTTGAAACCCTGTTCAACCTCCTTCTTGAAAGGGGATTT
+AAACATTTCTAAGGGATCCCTTCCTCTAATACCGGGCTTTCTTGGGGGGGCAGTCAAATG
+TTTCCCTGGGATTTGTTAAAAAAAAGGGAAAAAGGAAAAATCCGAACTTTTTGGCCCCCC
+CCAACCCCTGAAAAATATAAAAAACTTTTGGCTCCCCCCCCAAGAAGGAAAATTTTTTCG
+GTTTGGGATTTGGGGGGGCCCCCTCTCTTTTGGGTTTCTTTCTCCCCCTCCCTCTCCCGC
+AAAAAATTGGGGATTTTTTCCAAAAGCGGGGAGAAATTTTATAAAAAAAATTGGGGGGAG
+ACCCTTTCCCCTTTTGTTTCCACCCCCCCCCCAAAGGGGGTTTTTTTTTTTTTGAGAAAA
+CCACCCCACCCCCCCAACCCCCCGCTGGTAAA
+>AW4C2 [Astrosclera_willeyana]
+TTTTTTTTCAAACCAAATACTTTTTNTGAATGGTGTGTGCACAAACTCAGCAAAACAGAT
+ACAAACCTGCATGATCACACACTACATATGCATATCACAAGAGAAAAAACACACTAATCT
+GTTAAAACTAGTGTTGTGTACTAAGAGTTCAGGTTTGGGTGCTCAGAAGCACTTGCGGTG
+GACAATGGAAGGTCCCGATTCGTCATACTCCTGCTTTGAGATCCACATCTGCTGGAAGGT
+GGAGAGAGAAGCCAAGATGGAGCCACCAATCCATACTGAATACTTCCTCTCGGGAGGAGC
+AATGATCTTAATCTTCATGGTTGGGGGAGCCAGAGCTACGATCTCCTTTTGCATTCTGTC
+AGCAATGCCAGGGAACATTGTACTGCCACCAGAGAGCACAGTATTAGCGTAGAGATCCTT
+ACGAATGTCTACATCACACTTCATGATGGAGTTGTAGCAGGTTTCATGGATGCCAGCCGA
+CTCCATTCCCAGGAAGCTGGGCTGGAAGAGGGCCTCGGGGCACCGGAAGCGCTCGTTTCC
+AATGGTGATAACCTGTCCATCAGGAAGCTCATAACTCTTCTCGATGCTGGAGCTGGAGGC
+AGCTGTTTGCATCTCCTGTTCAAAGTCTAGTGCTACGTAGCACAGCTTCTCCTTGATGTC
+ACGCACGATTTCACGCTCTGCCGTTGTGGTGAACGAGTAGCCACGCTCGGTGAGGATCTT
+CATCAGGTAGTCTGTCAGATCACGCCCGGCGAGGTCGAGACGAAGGATGGCGTGTGGGAG
+GGCGTATCCCTCGTAGATGGGCACGGTATGTGAGACTCCGTCGCCAGAATCGAACACGAT
+ACCGGTGGTACGGCCAGAGGCGTACAGCGAGAGCACGGCCTGGATGGCGACGTACATGGC
+TGGTGTGTTGAAGGTCTCGAACATGATCTGGGTCATCTTCTCGCGGTTGGCCTTGGGGTT
+GAGGGGCGCCTCTGTTAGGAGAACGGGGTGCTCCTCGGGCGCAACACGCAGCTCGTTGTA
+GAAGGTGTGATGCCAGATCTTCTCCATGTCGTCCCAGTTAGTAACGATACCGTGCTCGAT
+GGGGTACTTGAGGGTGAGGATACCTCTCTTACTCTGGGCCTCATCGCCGACGTACGAGTC
+CTTCTGGCCCATACCCACCATCACGCCCTGGTGACGAGGGCGGCCCACGATGGAAGGAAA
+CACAGCGCGAGGTGCATCATCGCCGGCGAACCCGGCTTTGCACATGCCGGAACCGTTATC
+AACAACCAACGCAGCAACGTCCTCGTCGCACATTTTGAAGCGTGAAGTTAGGAGGAAGAA
+AGCAAGAGTACACACTCCACGATGCTCCAATCAAAAGAAAGTCCCTCGGTCCGAAAGCCC
+TTGGGGGG
+>AW5C1 [Astrosclera_willeyana]
+TACGGCCGGGTATCAGCTACTAAGGGCTTACGGTGGATGCCTTGGCGCCAGGTAGCGATG
+AAGGGCGTGACAAACTGCGATAAGCTTCGGGTAGTTGTTTAGTAAACATTGATCCGGAGA
+TCCCCGAATCGGGCAACCGGGCAGGCTTTGCCTGTCATCTCGGCGTAAGTCGGGAGGCTA
+ACCAGGAGAAGTGAAGCATCTCAGTAACCTGAGGAACAGAAAGAAAACTCGATTCCCCCA
+GTAGTGGCGAGCGAAAAGGGAATAGCCTAAACTGGGTATATGTTAAAGTCCATTTACGTT
+GTATACCTGGGGTTGTGGGGTAATGTTGGGCTTGAATATGGTCAAGCCGGGAAGTTATAA
+ACCAAGTTTTTAGCTTAATGTTTCTGGAATAGGACAACCAAAGAGGGTAACAGTCCCGTG
+AGCGAAAAGAATTTGGCTTCCTGAACGTTATTCCCAAGTACTATGGGATAGCCTAAACCT
+GTAGGAATCTAGGAGGACCACCTCCTAAGGCTAAATATGACTTGGCGACCGATAGTGAAG
+AAGTACTACaaaaaaaaaaaaaaaaaaaaaaaaaaaaGTgggggcccccccgcccccgcc
+cTTTTTTAATTCGAAAAATTTTTTTGGGGGGGCCCAATTTGGGGTCTTTTGGGCATTTTC
+CCCTTTTGGGGGGGGT
+>AW5C2 [Astrosclera_willeyana]
+TACGGCCGGGGANTTGGCGACCGATAGTGAAGAAGTACTGTGAAGGAAAGGTGAACAGTC
+CCCCCGCTAGGGAAGTGAAATAGTCCCTGAAACCGTACAGCCTACAAGCTGTGGAAGTGC
+TAAGTCTCGATCCGTCGAGACATGCATGACTGCGTGCCTTTTGCATAATGAGCCGGCGAC
+TTACTCTGTGTAGCAAGGTTAAGCTTTTCTGAAGCGTAGCCGTAGCGAAGGCGAGTCTGA
+ATAGGGCGATAGAGTTGCATGGAGTAgacccgaaactgggtgatctatccatgggcaagg
+tgaagcatacgtaaaagtatgtggaggcctgaacccaccaaggctgaaaacttgggggat
+gacctgtggatcggagtgaaaggctaatcaaacccagtgatagctggttctccccgaaat
+AGCTTTAGGGCTAGCCTCATGTGTTTGGCAGTGGTGGTAGAGCTCTGATTGGACTAGCGG
+CCCCACCAGGTTAGCAACTCCAGTTAAACTGCAAATGCCATTGTCTTAAAGCATGGGAGT
+CAGTCAGTAGGGGATAAGCTCTACTGACAAAAGGGATAAGAGCCCAGATCGCCAGCTAAG
+GTCCCCAAATACAGGCTAAGTGGTAAAGGATGTGTCGTTGCCCAGACAGCCAGGATGTTG
+GCTTAGAAGCAGCCATTCATTTAAAGAGTGCGTAATAGCTCACTGGTCAAGTGGCTTTGC
+ACCGAAAATTCTCGGGGCTTAAGCCTGTTACCGAAGCTGCGGATTTTGACCCACGTACCG
+GTTCGCCGACAGCGGGGTTGAAGTGGTAGGGGAGCGTTCTATAGTAGGATGAAGGTATGT
+CAAAGTACGGTCTTTCTATGTACATATTTTTAACACCTTCCCCTACTCTGGGAGTGATTG
+AAAACTGTAACCACCTAATTCTCTGTAATACCTGTGGTGCCGTGGAAAAGAAAAACCATT
+TTTTTTTAACTCCATTCTCTCCCCCAAGCCCCAAAGGATTAAACAATCGGAAAAAAGTTT
+AGTTTTCCGCTCCCCCATTAAAAGGATGAAAGTAAGGCACATCTAAGGCTTAAGCGATCC
+AACATGCGGAAGGTAGTGCATGGTTCACTCCCCAACAGAAGGGAACTTCAGTTAAAATCC
+GTAGTTTCATTAACTCTTAAAACGTTATCTGGATTCTCGTTAGGAATACAATCTGGTCCT
+ACTTTTCTACTCAACAAAAACAACCTTTAGTGGTACACGTAAATGTCCTCCCAAACTCCT
+ACACCGTACCCGGTGAGCTCAACTATAGAATCCTAATCGTGTCTCCATAAGAATTCTCCC
+TAATGATACCTACCCCAAAAAAAACAAAAGGAAAAAAAAAAAACAAACATAGGTGCTCCC
+TCTCCCTCATTAGACCCAATATATTCGACCAGCTTAATTTTTTCTCTCTCGCCTCTACTT
+TATCTTCATTTATTCTCCATCCCCCTCAAAGTAGAAAATAATAAAAAAAAATCAAAAACA
+CTTTNTTTAATCTCCATTTTCTCTTCTCTCCTCCCTCTAACACCTCCACAACACCAACGC
+CTTATATAACTTTGTAACACACACTTTGTAAATTACTACTAACCAATGTCATCATACATA
+TTTCTTATTCACTTACACCACATCCAAGCTAAACTAAGACTTCCAATTAGATATACCTAC
+CCCCTGAATGCATCCATTCTATAATCTCATCCTTCATCTCATAATCAACTTCGTTGTTCT
+CTGCCCACCCTCCATCTCTGTTCTGCTATCTCCTGCATTTCCTAGCTCTCACTCCATTCC
+CACCCCTGAACTTTCCTCTCTTTTCATACCCTACTGCTTGCCTTCTATTTTCTGACTCCA
+TTAACTTCGCTTCCATTAACTACTGCGTTCTTTCTATCTCTCACTAAACTGCACCCTCAC
+TCATTTCTTACTCTACCCCTCTCTCCCNCCCTTCATGCTTCTCTTTTAATACTATCCCAT
+TCGTCCACATCTCCCTCATTCATCG
+>AW5C3 [Astrosclera_willeyana]
+GGGTAATGTTGGGCTTNGATATGGTCAAGCCGGGAAGTTATAAACCAAGCTTTTAAATTA
+ATGTTTNTGGAATAGGANAANNAAAGAGGGCAACAGTCCCGTGAGCGAAAAGAATTTGGC
+TTCCTGAACGTTATTCCCAAGTACTATGGGATAGCCTAAACCTGTAGGAATCTAGGAGGA
+CCACCTCCTAAGGCTAAATATGACTTGGCGACCGTGAAATTGAGTTTGGTGGACCAGGAG
+CAAGATGTCAGAGAAGTTTGGAGACGTTCGTGTCCGTGATGCTGGCCAATATATTGTCAA
+GAACTTTCGCTCATTTCCTCAGTTTGTCGGTCGGTTGATACAGACCTACAGAGCAACATA
+CATCACCTGCAAGACTGTCCGAATGACACCTTACTTCCACATCGTTGGGGTGGCCATCGC
+AATAAACTATATGATTGATTACAAGTACCACTTGAAGTATGAGAAACTGCGCAAATACCA
+CTGAACATTGAACCAAGTTGTACTCACACCTTGTCACATCTGTATAGACACAAAGGTCCA
+TCATATGGTGCTGCATTGTATGCC
diff --git a/test/test_blackbox_extract.rb b/test/test_blackbox_extract.rb
@@ -3,13 +3,56 @@
 
 class BlackBoxTest < Test::Unit::TestCase
 
-  SPLIT_DATADIR = "test/data/extract"
+  EXTRACT_DATADIR = "test/data/extract"
+  EXTRACT_BINARY  = "bin/phyta-extract"
 
-  context "Command line output" do
+  context "Extract command line output" do
     should "print default message if run without parameters" do
-      result = %x[bin/phyta-extract]
+      result = %x[#{EXTRACT_BINARY}]
       expected = "Invalid arguments, see --help for more information."
       assert_equal expected.strip, result.strip
     end
   end
+
+  context "Extracting" do
+    should "work if the clean file is empty" do
+      Dir.mktmpdir do |dir|
+        result = %x[#{EXTRACT_BINARY} -c #{EXTRACT_DATADIR}/clean_empty_clean.csv -d #{EXTRACT_DATADIR}/clean_empty_contaminated.csv -f #{EXTRACT_DATADIR}/truncated.fasta -o #{dir}/clean_empty_clean_out.fasta -p #{dir}/clean_empty_contaminated_out.fasta]
+
+        clean_result = File.open("#{dir}/clean_empty_clean_out.fasta").read
+        contaminated_result = File.open("#{dir}/clean_empty_contaminated_out.fasta").read
+
+        clean_target = File.open("#{EXTRACT_DATADIR}/clean_empty_clean_target.fasta").read
+        contaminated_target = File.open("#{EXTRACT_DATADIR}/clean_empty_contaminated_target.fasta").read
+
+        assert_not_nil clean_result
+        assert_not_nil contaminated_result
+        assert_not_nil clean_target
+        assert_not_nil contaminated_target
+
+        assert_equal clean_target, clean_result, "Clean files differ"
+        assert_equal contaminated_target, contaminated_result, "Contaminated files differ"
+      end
+    end
+    should "work if the contaminated file is empty" do
+      Dir.mktmpdir do |dir|
+        result = %x[#{EXTRACT_BINARY} -c #{EXTRACT_DATADIR}/contaminated_empty_clean.csv -d #{EXTRACT_DATADIR}/contaminated_empty_contaminated.csv -f #{EXTRACT_DATADIR}/truncated.fasta -o #{dir}/contaminated_empty_clean_out.fasta -p #{dir}/contaminated_empty_contaminated_out.fasta]
+
+        clean_result = File.open("#{dir}/contaminated_empty_clean_out.fasta").read
+        contaminated_result = File.open("#{dir}/contaminated_empty_contaminated_out.fasta").read
+
+        clean_target = File.open("#{EXTRACT_DATADIR}/contaminated_empty_clean_target.fasta").read
+        contaminated_target = File.open("#{EXTRACT_DATADIR}/contaminated_empty_contaminated_target.fasta").read
+
+        assert_not_nil clean_result
+        assert_not_nil contaminated_result
+        assert_not_nil clean_target
+        assert_not_nil contaminated_target
+
+        assert_equal clean_target, clean_result, "Clean files differ"
+        assert_equal contaminated_target, contaminated_result, "Contaminated files differ"
+      end
+    end
+  end
+
 end