Added test for --nucleotide_output option

test/basic.nuc_out.expected

@@ -0,0 +1,133 @@
+>stx2_stop:694-1653 strand:+ stx2 INTERNAL_STOP
+ATGAAGTGTATATTCTTGAAGTGGTTGCTGTGTCTTTTATTAAATTTCTCTGCTATATCT
+TATGCCCGTGAGTTTACAATAGACTTTTCGTCTCAACAAAGTTATGTATCTTCGTTAAAT
+AGTATACGCACAGCGATATCGACACCCCTTGAAAATATATCTCAGGGGGGTACATCGGTA
+TCGGTTATTAATCATACGCCACCAGGAAGTTATATTGCCGTAGATATACGAGGGCTTGAT
+GTTTATCAGGCGCGTTTTGACCACCTTCGTCTGATTGTTGAGCAAAATAATTTATATGTG
+GCTGGATTTGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTTCACATATA
+TCAGTGCCCGGTGTGACAACGGTTTCCATGACAACAGACAGCAGTTATACCACTCTGCAA
+CGTGTCGCAGCGCTGGAACGTTCTGGGATGCAAATCAGTCGTCACTCACTGGTTTCATCA
+TATCTGGCGTTAATGGAGTTTAGTGGTAATGCCATGAACAGTGAGGCCTCCAGAGCAATC
+CTGCGTTTTGTCACTGTCACAGCCGAAGCTTTACGCTTCAGGCAAATACAGAGAGAATTT
+CGTAAGGCACTATCTGAAGCAGCTCCGGTTTATACGATGACATCGGAAGATGTGGACCTT
+ACTCTGAACTGGGGAAGAATAAGCAATGTTCTTCCTGAATACAGAGGAGAAGAGGGCGTC
+AGGGTGGGGCGAATATCCTTCAATAGTCTTCCGGCAATACTAGGGAGTGTGGCGGTTATA
+TTGAATTGCCATCATCAGGGGGCACGTTCTGTTCGCTCCGTTAATCAAGAGAAGCAACCG
+GAATGTCAAATAACTGGCGACAGGCCAGTTATAAAAATAAACAATATCTTATGGGAAAGT
+AATACAGCAGCAGCTTTTCTGAACCGGAAATCTCAGTCTTGATATGCAACTGGTAAATGA
+>stx2_fs:2165-3232 strand:+ stx2 FRAMESHIFT
+ACATCGGTGTCTGTTATTAACCACACCCCACCGGGCAGTTATTTTGCTGTGGATATACGA
+GGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAAT
+TTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTT
+ACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACC
+ACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTG
+GTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCC
+AGAGCAGTTCTGCGTTTTGTCAGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAG
+AGAATTTCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGT
+GGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGA
+TGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCGGCGATACTGGGCACTGTGGC
+CGTTATACTGAATTGTCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGATAG
+TCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATG
+GGAAAGTAATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGG
+TAAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCT
+GTTAATGCAATGGCGGCGGATTGCGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAG
+AATGATACATTCACAGTAAAAGTGGCCGGAAAAGAGTACTGGACCAGTCGCTGGAATCTG
+CAACCGTTACTGCAAAGTGCTCAGTTGACAGGAATGACTGTCACAATCAAATCCAGTACC
+TGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx2_novel:216-1456 strand:+ stx2 COMPLETE_NOVEL
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCC
+TATTCCCGGGAATTTACGATAGACTTTTCGACTCAACAAAGTTATGTCTCTTCGTTAAAT
+AGTATACGGACAGAGATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTG
+TCTGTTATTAACCACACCCCGCCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGAT
+GTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTG
+GCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATA
+TCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTCTGCAA
+CGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCA
+TATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTT
+CTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTT
+CGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTC
+ACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTC
+AGAGTGGGGAGAATATCCTTTAATAATATATCGGCGATACTGGGTACTGTGGCCGTTATA
+CTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGAGAGTCAACCA
+GAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGT
+AATACAGCAGCAGCGTTTCTGAACAGAAAATCACAGTCTTTATATACAACGGGTAAATAA
+AGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATG
+CAATGGCGGCGGATTGCGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAATGATA
+CATTCACAGTAAAAGTGGCCGGGAAAGAATACTGGACCAGTCGCTGGAATCTGCAACCGT
+TACTGCAAAGTGCTCAGCTGACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAAT
+CAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>stx1a:218-1444 strand:+ stx1a COMPLETE
+ATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTG
+GTGGCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAAT
+GTCATTCGCTCTGCAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTA
+CTGATGATTGATAGTGGCACAGGGGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGAT
+CCAGAGGAAGGGCGGTTTAATAATCTACGGCTTATTGTTGAACGAAATAATTTATATGTG
+ACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTGCTGATTTTTCACATGTT
+ACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCACGTTACAG
+CGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCT
+TATCTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATG
+TTACGGTTTGTTACTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTT
+CGTACAACACTGGATGATCTCAGTGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGAT
+CTTACATTGAACTGGGGAAGGTTGAGTAGCGTCCTGCCTGACTATCATGGACAAGACTCT
+GTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTCTGGGAAGCGTGGCATTA
+ATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGAGTTTCCT
+TCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGAT
+TCATCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATG
+AAAAAAACATTATTAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACG
+CCTGATTGTGTAACTGGAAAGGTGGAGTATACAAAATATAATGATGACGATACCTTTACA
+GTTAAAGTGGGTGATAAAGAATTATTTACCAACAGATGGAATCTTCAGTCTCTTCTTCTC
+AGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATGCCTGTCATAATGGAGGG
+GGATTCAGCGAAGTTATTTTTCGTTGA
+>stx2c:1298-2538 strand:- stx2c COMPLETE
+ATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGCTTTTCTTCGGTATCC
+TATTCCCGGGAATTTACGATAGACTTTTCGACTCAACAAAGTTATGTATCTTCGTTAAAT
+AGTATACGGACAGAGATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTG
+TCTGTTATTAACCACACCCCACCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGAT
+GTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTG
+GCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATA
+TCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTCTGCAA
+CGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCA
+TATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTT
+CTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTT
+CGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTC
+ACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTC
+AGAGTGGGGAGAATATCCTTTAATAATATATCGGCGATACTGGGCACTGTGGCCGTTATA
+CTGAATTGTCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGATAGTCAACCA
+GAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGT
+AATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGGTAAATAA
+AGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATG
+CAATGGCGGCGGATTGCGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAATGATA
+CATTCACAGTAAAAGTGGCCGGAAAAGAGTACTGGACCAGTCGCTGGAATCTGCAACCGT
+TACTGCAAAGTGCTCAGTTGACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAAT
+CAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGA
+>partial_contig_end:3-661 strand:- stx2 PARTIAL_CONTIG_END
+AGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGT
+CGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACC
+AGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTC
+AGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATG
+ACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAG
+TATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCAGCGATA
+CTGGGGACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCC
+GTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCTGTTATAAAAATA
+AACAATACATTATGGGAAAGTAATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTT
+TTATATACAACGGGTAAATAAAGGAGTTAAGCATGAAGAAGATGTTTATGGCGGTTTTAT
+TTGCATTAGCTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTT
+>partial:27-1048 strand:+ stx2 PARTIAL
+GTACACCTCAGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGATTATT
+GAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGT
+TTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGAC
+AGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGT
+CGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACC
+AGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTC
+AGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATG
+ACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCCGGAG
+TATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCAGCGATA
+CTGGGGACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCC
+GTGAATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATA
+AACAATACATTATGGGAAAGTAATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTT
+TTATATACAACGGGTAAATAAAGGAGTTAAGCATGAAGAAGATGTTTATGGCGGTTTTAT
+TTGCATTAGCTTCTGTTAATGCAATGGCGGCGGATTGTGCTAAAGGTAAAATTGAGTTTT
+CCAAGTATAATGAGGATGACACATTTACAGTGAAGGTTGACGGGAAAGAATACTGGACCA
+GTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGTTGACAGGAATGACTGTCACAA
+TCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACT
+GA

test_stxtyper.sh

@@ -47,8 +47,23 @@ function test_input_file {
 }
 
 
-test_input_file 'basic'
+test_input_file 'basic' '--nucleotide_output test/basic.nuc_out.got'
 FAILURES=$(( $? + $FAILURES ))
+# test --nucleotide_output option
+TESTS=$(( $TESTS + 1 ))
+if ! diff -q "test/basic.nuc_out.expected" "test/basic.nuc_out.got"
+then
+    echo "not ok: $STXTYPER returned --nucleotide_output file different from expected"
+    echo "#  $STXTYPER --nucleotide_output test/basic.nuc_out.got -n test/basic.fa > test/basic.got"
+    echo "# diff test/basic.nuc_out.expected test/basic.nuc_out.got"
+    diff "test/basic.nuc_out.expected" "test/basic.nuc_out.got"
+    echo "#  To approve run:"
+    echo "#     mv test/basic.nuc_out.got test/basic.nuc_out.expected "
+    TEST_TEXT="$TEST_TEXT"$'\n'"Failed basic --nucleotide_output test"
+    FAILURES=$(( $FAILURES + 1 ))
+else 
+    echo "ok: --nucleotide_output test/basic.nuc_out.got options worked"
+fi
 
 test_input_file 'synthetics'
 FAILURES=$(( $? + $FAILURES ))