bio-polymarker 1.3.2

data/test/data/test_primer3_error.csv

@@ -0,0 +1,4 @@
+Excalibur_c93405_296,6AL,gtacttcagccctagcatatcgaacctgaacctgtctttttagtgtggcc[A/G]CGGGTGGAGACGGAGGCTGGTAGCGGCTCCCCAGGAAGAAGACCTTCTTC
+Excalibur_c97559_331,5BL,CGCTGCAGCCTCCACGCCTGCCTGTGCACCACCGCCGGCGCCAAACGCGA[T/C]GTTTGGGACACTCATGAAATCCCGTGACGCCACTGGAAAGACGTAACTGT
+Excalibur_c9760_365,5AL,aagttctgattctttaatcgagataaaggagatgaggctgatcttccact[T/C]GAATCAGGACGCTGTGAGGCAGTACATCGCCCGCACCCCGAAGCTCCAGT
+Excalibur_c9761_475,4AL,ACATTTGATGAGCTGAAAGATGGCTTGAAAAGGGTGGGCTCAGAGCTAAC[A/C]gaacatgaaatccaggctttaatggatgcggcggacatcgacaacagcgg

data/test/data/test_primer3_error_contigs.fa

@@ -0,0 +1,10 @@
+>IWGSC_CSS_3AL_scaff_4441924
+catgaatttagnnnnnnnnnnnnnnnnnnngagagagagagagggagggatcatagtatgcatcgtccttcgcttatctagtgcgaggaactacagatagaaaggagaaatatgcttggcactgatggatatagaatgcagtgcatcataaccaaatatggacaaagcggcaatggctgtaaaagcaaccacgtgatgaaaatttgcaaatgggaacatggaacaaaaatagcaagagtttccatctcatgtacagtagtaaaggaaccctgaaaatggctgtaaaagcaatcacgtgaccgataacatactccctgtcgtaaaggaaccctgacatataaagttgtactatttcatcagataccttattagcgcagtagtacgtctttctagatgcctagaccccgcggccgataacatactccctgtcgttgcagaagaatggaaactgcacaggcaaggcaagcagtgaaggcaaaacttatatagtttgtaatgctttccagaaatattgccagggatatcacgcagatagtggcaaagcagtactacagcgggcattctagaatgaaacaaagtgaccaattttttaatcctaagctatagtatagtatcttgtatgtctaaacactgaataactgaaccaaatttcattgcaatcaatatcacaaatctacatatctcgtcaacaatccaaaaacagtacaataattgatataattttgaaaagttcagacaccgttgctcttgaattgtaaggctatgtctgaatcaactttgaaagactacacacacaaaattcttcagttatgcagtcgctcaactaaaaaactaactaagaaggcttcatgcatacctcgggatctcttctccaggcctggcaccgcatcgtcggcaatgtgtgttccatcatgtgtaggccgggccgccgtccttctcttcgacgaccctccctgcatcaagtccatgtgctcactgaaattgttgctccggcgccacagaagccgcctttgctctacacgatttacaatcaaatcaggcgaccacaacacgcacacacaggccgcaccctctgcctgtagccgccggctcgcgtgcaccctcaagcacaaacctgcatgcacctctgccgactggcctctgacgcatacgctctgcaatacactgagtttgaggggatgattacataattctgaaaaggttcaagaattgtatatcttttaaaagcataaacaacatatttcagaatctactagtgcaaaacttacacattcacaactttccctttagtagttttttaaatgcataaagaacatcatatttctcatgggcggcctgctggttgcacaaatactccaggagaaccatagctgattagtttcacttctttctagatttccattttgcgctagtccaccaagtcctccaccaatatccgtgataaccccgtggcacggtaagtgaaggatacatcacaaatactctgaaaaaggatgaaaaataaacataattgtcaaatgaagatattattatgtaaatggaacagccggagaggcttacgttcaagctgaaagagccatgatcccacaggtcctaatccgtcccttcgtgtaaataacaatggaattgatacagtgctttaatatagcatttgacaaacaataagcaagaagaggattgatgcttcattctctaatacatgtctttagttcctgcatacacactggacggatttaattcagatgaagataaggaaaaacgggtgcacccttcctatgcacatggcatatccattagagaattagtggcagtggttaacctaaagagtctggaattacattacacaaaaagagaacagggaaatgtgtagacatcatatcatacagctagaatgctaaatgttgctcctaactgaactgaactaagatggcagccaaatctgaacttgaactcaactaaatggctacttgagctaatataattggtccaaaaaggtcattttaaaactgtatcggagataaccatggaaataatttatagaacataaaaaagaaaaacaacatttagcttcttgtaaccgtacaagtggcaggaatatacaaacagaattatctttgggtgcccaaaacaacttcacttcaattactcactatacaatttggttctgtagaatggtagatcagaagtttctttctggttgatacaataactatgcatgaggtgctagctccagtaaagtagtatatgttagttctaccagattgcaataatatcggataagcctccaaataggtgcatgttgacaagaaaatatgactggtatactaagtattcactataacatgcatgctttcttaatggtaatatttgttgatttccatattctgcaaatacgaacgactgatgctttcccaccacgaatacattttgtactnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncaatagcaccgtacctacagagtctctcgaggtctttctttaactcaggagcgtacttcagccctagcatatcgaacctgaacctgaaaacaacgattgtcggtttaatagatagtgcatatgcacaaccaagtgatagtttaactggacatcaaaatcccgttgtccacaggcgtaatttaaaccctgccgggcatgaagatcatgacacacaccattctaagaaaactaagaaattttatttgtcgtggatgtggtggtgagaacacaaaacagcaggggcacaccaagcagacgtgcacagcagcagcaaccagcaacatccacacatgcacattagcaagcaagtattgagatctgccaaggccgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnncttgaccatacgtgcagtagggaatatgtcgagggcgcggcggcgtacctgtctttttagtgtggccgcgggtggagacggaggctgg
+>IWGSC_CSS_7AL_scaff_549424
+ttttgtgttctcaccaccacatccacgacaaataaaatttcttagttttcttaggatcatgtgtgccatgatcttcatgcctggcagggtttacatgacgcttgtggacaacaggattttgatgtccagttaaactatcatatggttgtgcatatgcactatctattaaactgacaatccttgtttttcaggttcaggttcgatatgttcagggctgaagtacgctcctgagttaaagaaagaccttgagaaactcttagtgtgttgttgtcagtactactccaatactttggtgtggggttgcatagtactccaataatttagtgtggggtagtaaaaaatgtgttcgtggtgggaaagcatcagtggttcgtatttgcagaatagggaaatcaataaatattaccattaagaaagcatgcatggtatagtgaatacttagtataacagtcatatcttcttgtcaacatgcacctatttggaggcttattcgatattattgcaatctggtagaactgtgttactactaagaattgaatatttttagttggaatactattttaatgatcaatcacaatgttggacgcgaccacctatttattcccaagactttaagtcttgggtggcttaagcacaatatgccaggcatatgttctacatctgtggcatgtaatgaccctactggcatttcaagaggtcttgtaaatacaaaaataagtgttcactgcgtgagatttattaaatgttttagatatctcgcttgtggatgctcacccgtagctaatatcctgagtatattgataacaggtttaggtctggacggttattgagcctgcattgatgaaatagttgacaaagaagcaactgaaatgaggttattgagcctgcattgaagaatcttggttgatgagctgatatctgaccaaaaactcaagaactagaagcaagcctgacatcctttttttgtaatcggtatgttctcggtagcaagcctgtcatccttttctatccacatgaggcttactattttttacttgttgtcaccaatcaataaaacattgtgtattcattgcatatggtgaatggccttctagatttgtaagttcataggtagttatacaacagcagagccatgttctaaaaacagattcgagcctttccttggtttggagttgggccccgacgaaacgtccgagcgcatgaaatcagttcttttcaagaatgcaactgctttttttctctcatagtttccacccgtaacatatcacaagtatctttagtctaagaaagtaagaaaagtgaacttacatgatttttttaaattactaaataacttacaagataatgtatatttccgtttgagcattccaaaaactgaatgacactccattaagttgtaggatgcataaggtaagggaaatataggaagccaagacatctgtagtaataccagaagtggaagaacaagggcaagaaaacatttaaaagggccaatgataggcggaaaaagattcacgtggttaatagtcatgttttacaccaaggaagaacagaggaatggaaccaaagagaaatgagtgagcatacacctttgctagattttatgaactggactaatgtacaaaaacacacattgtcatcttggtgcatgtagatatttaatttaacaaattgaattccacatgaagcatactatactggacttctttgggctttacatgtgctcatattccataattcggatcagaaatgaagcctatgtgtatgtataaagcatttgcattatactaatattgtgtgtgttgtttttaatgccaaaggtaaatctgaacctgctcagaccacggggaggatttctctggtggactatcgctggcaaggttggcatgggagtaggcccgtaccatgggttcgtgcagctggagaaccgtggctagtgttgcgattgcctaatgtccatgtggagcataactcggcatgaggtgatatccttttatgataacctagctgtacacaatttcttcaaagaaaattaagattgatatcaaacttgagatcttcaatgtatttaaattagttcttaaattgctccaaagctactgaaatctcccttattatatttttctgtagatactgattgttctaattaaactcaccacttaaattccatagaaatgagaggctcaaggaagcaacaagtaggatgaaggagttaacgggcagaagcatagatcacagaaaaacaagaatatgttnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngctttgtatctcagtatgttcagagtggcttcaatctacaatttaaaaaggtgaatattggttggatcatgacacaagtgatgtggcttcagtcatgtttcttaagctaccgtggttatatcatcactaggccatatagcttaccaataaccttcttaagtacttccactgaaccatcatgattgccgactaatttttgtgttcatggttatatttcagagaaccggttcaaagaaatgtgaacactggttgggggttctaagaaggatgaccctaaatgggagcatgacagacaccgtggtccaggaaataagggggaatctcgtggtgtctactatgctttcagaaatcctatgcagtcaaggagattccttcagatttttgcatgatgagcaggtagttgtaaagggtcgtggtgtctactatgcttatcagaaaagtgagtgcatttgtgaagcttcctgcagagtttcacatgatgagtaggtaaatgtgttgcttgtgcatttaccaagtagttatataggagagcacacaagcaacagaccacacatcttgtgctaatttccatgataagttttagcacatatgaacaagttatagtgccagttaagttatgaatagaaattgagttgcttatcattgagtaaaagacgttcctttagagtatttatagttttatactaatactttatcaaggtgatatgctgaagatttgtgattatcatagtatggcctttacattgcttctgtatgatctgacctgttgagctcatcacaaagaccataaaaattggctctatccctgatgtacaataaaaaaggggaactatagcctcagatcaaaaaattttcttttcctatgtgattttgcagcgggacttgcttatggagacattcgctctgggtcaaagcttaagaggactgatgcttttgaccatttaattagtgtttaggtatgccctcctctcctttcccttcagctggaatctctgataaggttgtaatttgctggtgcagtgctgctctgcttttatttgtggatttctttgggatctaattttgaactgtcaaaactggtttgttgggtgccggttggtttaacatgatgctataatgccgtagagagagatatgtttttccagtagaagtggccggttagttaatttgagatttgtgccttttgttcttcaggcctgaagcttttggtttcaggccgacagttaaaagttgcattggcttgtaaaaaacttcatgtgactggaccagtagggggaggatagcttcatatggaaaataattctccatggtgggaaaatttgttatttgacatgattatatacagagatacaactagcagtgtttaaatatgggttcatctcaacctatgattcctatgtatataatttttggggctagaact
+>IWGSC_CSS_6AL_scaff_5756048
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+>IWGSC_CSS_3AL_scaff_4451587
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caagatgtccggagcctctcttgtgaatcacattgcttacaatgatttcatgattgagatgttgggatttgaacaagatgcatcttttaaaggtgtgactgtagaagtttagctaaataaacagaatatatctactgcaagttgatatatagaaaagtggatttttgcataggttttgtatnnnnnnnnnnnnnngttaagtcggtacttccttttctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnccgttgatttaatcaccgttgtctgtgatagacgttcacagatctggatgcctttgcttgccaaataaaatatgaacaataattatgttaggaagttacactagctttgacgatccgatcattcatggaatgttttccggcattgccaacatattgagtacttcagttgtaagtctgtaagcagttctctttgaaagagaaaaatgcatacatgcttcagtgaatggccacccccttctattttagtaacactgcacttcttagtagtacttgctaatcagtatggttattggtctgtaatcttattgtttctacattaattctttgtacgtaggccggatcaagcgcatcgccgatgccacgatcgccggtctgccgtgttactcctctcatgtgcgccctcgatgctgacgccgtcctattttccgcagccaccgccgtcgggctccgcgtccacgtgcgccttcaaacctactggatgcaatctcgcattgcgctgtcatccgcactatctggcaccacctatggacacagaacgacggatcaaggtttaatgactttgatcaggcaagatacattctgcccgctcatctccccgtgttgccgttggtaagtatggtagtattctcgatgcttcttttagtgcttctctctaaattcgttgggatccaattttgttcctgcaaaagttgcttgtgttctgtataggtgtacagttttcatgttaactggaaagtaccaaagttatctatcctagcggcatcaaactacaattttcttgttttattaataatttaatatgagatatacaagaaagtgcagcgggcatggcttgtactcatgcttgaggatatttggcttaggctcctggactgtgtcatggccacactgaagacgggacacttgtggttatcttcatgtgtcattggtggtcagagaaaccaaacaaagctggagtgaaaggtctatgagtttcaatacagaacaaagggtctacgagtttcaatacattgtcgaaaaattgtgccaaacattaaggttgatttcagttccttcatccttctagagcataagaaaaatatggttctttgcttgaaaaaattatggcttaattctggaaagcattaagtttccatgcatgctcatactgatcaatccataactctaaaaacatgataccctctttcacatgcttcatataagttatgcacatgccatctcgctaagcactgataacatgtttcgtttaacagatcatctaagatttgcataattgttttgagaatgagcagaacagcatcgacatcggcctcgatcggtgtcggggcaatggtgaaccaatgaagaagcttaaggcggctcaggtagggtggcacacgatattgacatcgaccacgaccagcgtcggaggatgggtcattgggacggaaggaggaagacaaagaggaggaagaagacgatgatcacaaaattttagcactgataaaaaacatgcggtcgatgcatagttgctcttgtagtatctgctaaagaaattcataaaatatgatatatattcgtaggacttcactc
+>IWGSC_CSS_5BL_scaff_10844348
+gtgttagtgcctacatgcagttttgaacattactacatgcctagctatttggtttgcaggatttgtaaaatgcactaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaacattcagaaatcgtactacattgtcattgtaaacttggaaaaaggtgtcacaaattgaactcccttatggttaacatttaacaggaaaggaacatcacctcgacatatagcttctccaggcatggaaagcatctcaggaaactgacaacttgctccaggtcgggcccgacagattctacttccaagaccttcactgtgcgcagtttcagggtcaagcttgtcggaatcattttctgaatgacagacgaacaaacatctttaaaattagaaataatgttaatttgtagaaggagaggtagaaggcggttgttgtacctgaacgggtgtggatccaataacaggttcagagtatttgtcagacgagtagctcannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcggaaaatgccaatgacggccgagccacaggtaggccggtatctgggccgtcctgccaccatggggatgtgcgctgttagagtatatgtcttgtatttgatttatttttgaactgtattgagtcaggtaggtcccaggcacatgcaaaggcatctaggcttctcacacgcctctgacatttatggcgatctggtgcatgtccatgccgtacgtcctggtgcatgcatggcctggcctggagcatgtgtgtccaacggagaccaccaattcaccgagtgcggacgtggagcatgggtgaccagcgaacagataagtttggtcaccattagccatcattcattagtcaaatcatgttaatgtgatcactcaggccgaactaacaaaacgagtcaggggtagatagtatgtgtgctaacatgtgaatggattttatctgttttacagactaaaaaatcgcacagattaggtacagactcgctaacaagtatgtgatggaggcatggagctaatagtttcaaaatcacacgtttcgtgttgacttaacacaccaatgcgacattagtgatgtcactttacgcgggcgcgcgcagtgtatctatgcagatttcttgtcgcccaactgccggcgttgcgcggcaggaaagcagcaccatcatttctaggagaaaagtttttgggagcagggcttccatcagttgtcacctcgtactaccagcggctaaatttcgtgttttgacttttttcgtaacttattcgaaatctgactctagttcgtaaaaaattcgagatctgacccttttctnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgnnnnnnnnctaagtatggaacacagtgcacgctcgcacctaccgccggacaccttggcggtagggttgtacagcctaccgccagcctgtttggcggtaggggtctttcttaacgccaggggccttggcggtaggctgttataccctaccgccaagggctttggcgataagaaagggttagatcccaaaatttttatgaatcggggtcagacctcgaataggtttcagaaaagggtcaaaacatgaaatttagccactaccagcacatgcactcatcgagcacgcacactacttagccgtgacagaccaggcggtgtggtgcacgagcaaactagacgagaaacgcacaacacaatgtgttaacacccgccaaaaactgacacggaatacttattagcacggagtactattaatttcttttcgctcgtaggtcgaaacgtcaaaaattcaggtaaaacatcgttcacttttcgggtgattagcaactcgttggcgaagagcatataactgaagcccaacagaaacaaaatgcaggcatgtgtagttaacaacagccacaacaacatttgaattgagttcctgcctaccaaagctaagtagtggcatgatatcaacgccacagttttgaactagcggttacgtaaactaacagccccatgatttaacatgcagtttacatagtagaccaaacaacaattcagggaagggcataaaagatagttctggttgtgcccaacaacaccacgtttgataaacttcggcgctgttttcacaactggaccatcacccttctctgcataagcacgcacagaccattgtagcgatgttttcctgttgggattcatctccctctcctcaggagccctgccgatccttatcctgaacaattgggttagcaacatatcaacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaatagatgcaagttatttttttgctcatggcaaacatatgcactcccaacagttacctataactaaattcagcacaaagaataaaacacctataccatcagcttggtcgcacgttccgctgagccacaaacaaataatcttactacttttggctgtgtcaaaaacacagatataagaccatccacaatccagaattacaactacctaggtctatagctgcacattgacagtatcttcatgccaccaaataatccagtcctctttctgagaacaccagcatctaaatccaaatacagataatcaactgtttgttcctttcaatgcatacacatcaccggtgcattattacaactgaatccacaccttcagtacatctgaacccagtaattacaacatccactcgagcatataaaccgcaaagatctatcaaggataataacagtttttccatctaacaccaccaacagaatgcatcatcccagtgctcccctaaaaattaatcatgtacacaaatccaaccaccatactataaaatccaaccacatgtgcaaaaatcttcaatctccaaacacctgtggagttttcaaatctcgagttatgcaaagaatccaactaccccactattaatcaaagagccactaggttagtgctaacatcagtggcgctgcaattccaacaatctatattaatcaaagagctctacattttcatacccagaactctttttttcgaaaatgatccacggcatgtacaactagcacactaccggaacagtacaaatatgtgcagaacatactatgaatcgccgcagaaacccaaaatcaactcttctgcacactagcaacataaacatgattcagatctaacttcgcacggcactccaaagaagaattgtggcagagcatcagcacactgacctccgttgtccagccactggtggcttcagagcacacctcgcccgctgcagcctccacgcctgcctgtgcaccaccgccggcgccaaacgcgatgtttgggacactcatgaaatcccgtgacgccactggaaagacgtaactgttccacggcgagggcgcagcacacatcctgcatgaatcgaagccgagccaaatcggttagaaatccccaaaatctgcggcggtaaacagacacctagatcaagagagggttggccggagggggagcatacatacccgttgagctgaggccattggtggaaatctcgccggagcagcacaggcgccgccgttcgccagatggggatgggggtggaggagccgacccgctgcgtggctctggtttattccacgcagacacaggccgcagtatcgtcgtggggacgcgggtgactagggcaagattctctcgcctgtgctgtttcgaacgataagtcatgggccgcacacaataggccagtactaggcgccggtccgccggcgctaggttcggccggtcagaccccagccgttcgatctggtacagtacagccgtccaaaaaaatcattcgtcccgatctagccttcccttccgtcttcttcctcccaacgaatcccaaataaaatcccacgccgctgtccccgcggctccgccttcgtgtgcagctcggcgaggggaacgactgccggccgccgcgcgcttgcacctctattccttgtagcccctctgctgctcgccggagaaccttctcgctagttaattttcagttacaagctccacctcagagttgcaactcccccgtcaacgctccatggttgtggcacccaatgtgtcgcctccgccactcgtcgtcgaccctcgctgcgactgacgaccaccattaaacgacattgagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtcaccgtcatcgcgggggcgcaggtccgccatgatgaatgtagcaaaatcgtttgccggttgcagctttttgagccgctgcttccagctttttgcatcaatggttccaacattggcagcgacggcgtggttgcagctcgcggaccgccgaccattgattagccgatgtgcaggttacagcttgccgaccaccggatgtagcaccgcctgatgccggttgtagcgccgcagccgtggggaggcaagagctgcgcgagcaccgcatcagcaaagtcgctcctcgggaaagattgacgtgcttgaccaccatggcttgcagtctggaggaaggggatttgggaggaaagagatgggaaaaaacaagtggacgctgttgtcttggggaagataagacaaagaaggaagcggtgcgtgtggggccggagtgacgtgttgcatgctcgatggcgcaaagcgcgttagcgagcgaggcgtccggcccagtttcggccggttcgccgattacaaacgtttacccacacaatacgcctacacattccctagccgtatcgcaggctgtatttcactacatagacctgccacccactgacggattgcacatcccaaggctcaaatggacgcccatgataccggcctacatgtggctcggcctctgaaaattcgcactagcgttacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnng

data/test/test_bfr.rb

@@ -0,0 +1,135 @@
+
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+tmp_verb = $VERBOSE
+$VERBOSE=nil
+#puts path
+require path
+require 'bio-samtools-wrapper'
+require "test/unit"
+$VERBOSE=tmp_verb
+
+
+class TestPolyploidTools < Test::Unit::TestCase
+
+  
+  #Set up the paths
+  def setupre
+    data_path= File.expand_path(File.dirname(__FILE__)   + '/data/' )
+    
+    @ref=data_path + '/S22380157.fa'
+    @a=data_path + "/LIB1721.bam"
+    @b=data_path + "/LIB1722.bam"
+    @f2_a=data_path + "/LIB1716.bam"
+    @f2_b=data_path + "/LIB1719.bam"
+    
+    @bfr_path=data_path + "/bfr_out_test.csv"
+    @fasta_db = Bio::DB::Fasta::FastaFile.new(fasta: @ref)
+    @fasta_db.load_fai_entries
+    @bam_a =  Bio::DB::Sam.new(fasta: @ref, bam: @a)
+    @bam_b =  Bio::DB::Sam.new(fasta: @ref, bam: @b)
+    @bam_f2_a =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_a)
+    @bam_f2_b =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_b)
+   # puts "SETUP"
+  end
+  
+  def teardown
+    
+  end
+  
+  def test_snp_between_consensus
+    setupre
+    
+    reg="gnl|UG|Ta#S22380157"
+    region = @fasta_db.index.region_for_entry(reg).to_region
+    min_cov=20
+    #puts region.to_s
+    
+    #puts @bam_a.methods
+    ref_seq=@fasta_db.fetch_sequence(region)
+    reg_a = @bam_a.fetch_region(region: region,  min_cov: min_cov, A: 1)
+    reg_b = @bam_b.fetch_region(region: region,  min_cov: min_cov, A: 1)
+    cons_1 = reg_a.consensus
+    cons_2 = reg_b.consensus
+    
+    snps_1 = cons_1.count_ambiguities
+    snps_2 = cons_2.count_ambiguities
+    
+    called_1 = reg_a.called
+    called_2 = reg_b.called
+    
+    snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
+    #block_size = 1000
+    #snps_per_1k_1   = (block_size * snps_1.to_f   ) / region.size
+    #snps_per_1k_2   = (block_size * snps_2.to_f   ) / region.size
+    #snps_per_1k_tot = (block_size * snps_tot.to_f ) / region.size
+        
+    snps_tot = Bio::Sequence.snps_between(cons_1, cons_2)
+    snps_to_ref = Bio::Sequence.snps_between(cons_1, ref_seq)
+
+    assert_equal(ref_seq.to_s, "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatctttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggtggcggttccgtcgccggaggagtctaaggccctcgttgtcgccgagaatgacgctgagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtcgcgaccgagaagaggatttcgctgatcaaggcatgggaggagaacgagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcggaangagaagcgtgccgcggcggaagcgcggcacggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaagcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
+    assert_equal(cons_1.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggaggaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggagtctaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcrcggcgaggagatcgtcgcggcggaggagaccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaggatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")  
+    assert_equal(cons_2.to_s , "acgcttgaccttaggcctatttaggtgacactatagaacaagtttgtacaaaaaagcaggctggtaccggtccggaattcccgggatatcgtcgacccacgcgtccgcgtccgaccagcacaaacaagactgtactctgggctcctctgactccgtgtcttgctaaaatatytttggtcgactcgttgcgaggttgatcagatggcggasgaagcgaagcaggatgtggcgccacccgcgccggagccgaccgaggacgtcgcggacgagaaggcggcggttccgtcgccggaggartcyaaggccctsgttgtcgccgagaatgacgcygagaagcctgcagctacagggggctcacacgaacgagatgctctgctcacgagggtygcgaccgagaagaggatttcgctgatcaaggcatgggaggagaaygagaaggccaaagccgagaacaaggccgtgaagttgctggcggacatcacctcgtgggagaactccaaggccgcggaactggaagccgagctcaagaagatgcaagagcagctggagaagaagaaggcgcgctgcgtggagaagctcaagaacagcgccgcgacggtgcacaaagaggcgraaggagaagcgtgccgcggcggaagygcggcgcggcgaggagatcgtcgcggcggaggagrccgccgccaagtaccgcgccaagggtgaggcgccgaagaagctgctcttcggcagaagatagatatcgcttcatcttcagcttctctctgtttgaccgnttgcatgtctcctgcccatggcatcacttgtgtatttatctttgggggngatcttagtttgtatggtatcatcaaatgcgtcgtga")
+    assert_equal(snps_tot , 6)
+    assert_equal(snps_to_ref , 12)
+    assert_equal(snps_1,10)
+    assert_equal(snps_2,13)
+    assert_equal(called_1,617)
+    assert_equal(called_2,612)
+  end
+  
+  def test_bfr
+    setupre
+    container = Bio::BFRTools::BFRContainer.new
+    
+    container.reference @ref
+    container.parental_1( path:  @a )
+    container.parental_2( path:  @b )
+    container.bulk_1( path:  @f2_a  )
+    container.bulk_2( path:  @f2_b  )
+
+    i = -1
+
+    container.init_counters
+    output_file =  File.open(@bfr_path, "w")
+  #  puts "Range: #{min}:#{max}"
+    assert_equal(@fasta_db.index.entries.size,1)
+    reg = nil
+    @fasta_db.index.entries.each do | r |
+      i = i  + 1
+       
+      reg = container.process_region({:A => true, :q => 37, :region => r.get_full_region.to_s,:output_file => output_file , :min_cov => 5} )
+      #puts reg.inspect
+    end
+    
+    with_bfr = [210, 297, 300, 645, 674]
+    
+    bases_1 = Array.new
+    bases_2 = Array.new
+    bases_1  << {:A=>0, :C=>24, :G=>147, :T=>0}
+    bases_2  << {:A=>0, :C=>33, :G=>142, :T=>0}
+    bases_1  << {:A=>35, :C=>0, :G=>142, :T=>0}
+    bases_2  << {:A=>25, :C=>0, :G=>149, :T=>0}
+    bases_1  << {:A=>0, :C=>32, :G=>0, :T=>146}
+    bases_2  << {:A=>0, :C=>24, :G=>0, :T=>152}
+    bases_1  << {:A=>22, :C=>0, :G=>38, :T=>0}
+    bases_2  << {:A=>49, :C=>0, :G=>20, :T=>0}
+    bases_1  << {:A=>26, :C=>0, :G=>16, :T=>0}
+    bases_2  << {:A=>36, :C=>0, :G=>10, :T=>0}
+    i = 0
+    with_bfr.each do | pos |
+      #puts pos
+      assert_equal(bases_1[i], reg.bases_bulk_1[pos - 1 ] )
+      assert_equal(bases_2[i], reg.bases_bulk_2[pos - 1 ] )
+      i += 1
+    end
+   
+   
+    
+    output_file.close
+    
+  end
+  
+end

data/test/test_blast.rb

@@ -0,0 +1,47 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+#puts path
+require path
+require "test/unit"
+
+class TestBlast < Test::Unit::TestCase
+  Query  = File.dirname(__FILE__) + '/data/' + "BS00068396_51.fa"
+  Target = File.dirname(__FILE__) + '/data/' + "BS00068396_51_contigs.fa"
+  Blast_file = File.dirname(__FILE__) + '/data/' + "BS00068396_51_blast.tab"
+  #Set up the paths
+  def setup
+    File.expand_path(File.dirname(__FILE__) + '/data/')
+  end
+  
+  
+  
+  def test_blast_to_exo
+    lines = File.readlines(Blast_file)
+    expected = [
+    "BS00068396_51 0 101 + 2AS_5222932 3015 2914 - 99",
+    "BS00068396_51 0 101 + 2DS_5334799 6812 6913 + 99",
+    "BS00068396_51 0 101 + 2BS_5245544 4549 4651 + 87",
+    "BS00068396_51 101 0 - 2BS_5163353 7425 7323 - 87"]
+
+    expected_v = [
+      "M 101 101", 
+      "M 101 101",
+      "M 69 69 G 0 1 M 32 32",
+      "M 69 69 G 1 0 M 32 32"]
+
+    lines.each_with_index do |line , i|
+      tmp =  Bio::DB::Blast.to_sugar(line)
+      assert_equal(tmp, expected[i], "Error in line #{i} of the SUGAR")
+      tmp =   Bio::DB::Blast.to_vulgar(line)
+      assert_equal(tmp, expected_v[i], "Error in line #{i} of the Vulgar")
+
+      tmp =   Bio::DB::Blast.to_exo(line)
+      puts tmp
+    
+    end
+    
+  end
+  
+end

data/test/test_exon_container.rb

@@ -0,0 +1,17 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+#puts path
+require path
+require "test/unit"
+
+class TestExonContainer < Test::Unit::TestCase
+  Query=File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
+  Target=File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
+  
+  
+   def test_simple_container_test
+     
+   end
+end

data/test/test_exonearate.rb

@@ -0,0 +1,48 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+#puts path
+require path
+require "test/unit"
+
+class TestExonerate < Test::Unit::TestCase
+  Query  = File.dirname(__FILE__) + '/data/'+"BS00068396_51.fa"
+  Target = File.dirname(__FILE__) + '/data/'+"BS00068396_51_contigs.fa"
+  #Set up the paths
+  def setup
+    File.expand_path(File.dirname(__FILE__) + '/data/')
+  end
+  
+  
+  
+  def test_simple_align_array
+    alignments = Bio::DB::Exonerate.align({:query=>Query, :target=>Target})
+    assert(alignments.size == 4, "The count of alignments should be 4, it was #{alignments.size}")
+  end
+
+  def test_parse_alingn_line
+    line="RESULT:\tBS00068396_51 0 101 + 2BS_5163353 7425 7323 - 462\t96.04\t101\t11974\t.\tM 69 69 G 0 1 M 32 32"
+    aln =  Bio::DB::Exonerate::Alignment.parse_custom(line)
+    assert(aln.query_id == "BS00068396_51")
+    assert(aln.query_start==0)
+    assert(aln.query_end==101)
+    assert(aln.query_strand==:forward)
+    assert(aln.target_id=="2BS_5163353")
+    assert(aln.target_start==7425) 
+    assert(aln.target_end==7323) 
+    assert(aln.target_strand==:reverse)
+    assert(aln.score==462.0) 
+    assert(aln.pi==96.04)
+    assert(aln.ql==101)
+    assert(aln.tl==11974)
+    assert(aln.g==".")
+    assert(aln.vulgar_block.join(',')=="M	69	69	0	69	7425	7356,G	0	1	69	69	7356	7355,M	32	32	69	101	7355	7323" )
+    assert(aln.line==line)
+    
+    #puts aln.vulgar_block.inspect
+    #puts aln.inspect
+  end
+
+  
+end

data/test/test_integration.rb

@@ -0,0 +1,76 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+tmp_verb = $VERBOSE
+$VERBOSE=nil
+#puts path
+require path
+require 'bio-samtools-wrapper'
+require "test/unit"
+$VERBOSE=tmp_verb
+
+
+class TestInregration < Test::Unit::TestCase
+
+  
+  #Set up the paths
+  def setup
+    @data_path= File.expand_path(File.dirname(__FILE__)   + '/data/' )
+    
+    @ref="#{@data_path}/7B_amplicon_test_reference.fa"
+    @amplicon = "#{@data_path}/7B_amplicon_test.fa"
+    @genomes_count = 3
+    @output_folder="#{@data_path}/test_out"
+    @bin=File.expand_path(File.dirname(__FILE__) + '/../bin')
+    @marker = "#{@data_path}/7B_marker_test.txt"
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+
+    cmd = "makeblastdb -in #{@ref} -dbtype nucl "
+    #status, stdout, stderr = 
+    systemu cmd
+    # @ref=data_path + '/S22380157.fa'
+    # @a=data_path + "/LIB1721.bam"
+    # @b=data_path + "/LIB1722.bam"
+    # @f2_a=data_path + "/LIB1716.bam"
+    # @f2_b=data_path + "/LIB1719.bam"
+    
+    # @bfr_path=data_path + "/bfr_out_test.csv"
+    # @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
+    # @fasta_db.load_fai_entries
+    # @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
+    # @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
+    # @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
+    # @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+   # puts "SETUP"
+
+  end
+  
+  def teardown
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+    Dir.glob("#{@ref}.n*").each do |file| 
+      #puts file 
+      File.delete(file)
+    end
+  end
+  
+  def test_amplicon_primers
+    cmd = "ruby #{@bin}/polymarker_capillary.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+    assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+   
+  end
+
+  def test_deletion_primers
+    cmd = "ruby #{@bin}/polymarker_deletions.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+  def test_polymerker
+    cmd = "ruby ./bin/polymarker.rb -m #{@marker} -c #{@ref} --extract_found_contigs  -A blast -a nrgene --output #{@output_folder}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+end

data/test/test_snp_parsing.rb

@@ -0,0 +1,121 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bio-polymarker.rb')
+
+#puts path
+require path
+require "test/unit"
+
+class TestSNPparsing < Test::Unit::TestCase
+
+  #Set up the paths
+  def setup
+    @data = File.expand_path(File.dirname(__FILE__) + "/data")    
+  end
+
+  def test_snp_sequence
+    snp = Bio::PolyploidTools::SNPSequence.parse("BS00068396_51,2A,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+    assert(snp.gene == "BS00068396_51" )
+    assert(snp.chromosome == "2A")
+    assert(snp.sequence_original == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+    assert_equal(snp.position ,  51, "Position isnt parsed #{snp.position}")
+    assert_equal(snp.original , "T", "ORiginal base not parsed, is #{snp.original}")
+    assert_equal(snp.snp , "C")
+    assert(snp.template_sequence == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA", "#{snp.template_sequence}!=CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
+  end
+
+  def test_mutant_snp
+
+    ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
+    fasta_reference_db.index
+    fasta_reference_db.load_fai_entries 
+    
+    snp = Bio::PolyploidTools::SNPMutant.parse("IWGSC_CSS_1AL_scaff_1455974,Kronos2281,127,C,T")
+    assert_equal(snp.gene , "1AL_1455974_Kronos2281_127", "The original name was not parsed: #{snp.gene}")
+    assert_equal(snp.contig, "IWGSC_CSS_1AL_scaff_1455974")
+    assert_equal(snp.chromosome, "1A", "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(snp.position, 127, "The position is not parsed: #{snp.position}")
+    #snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
+    region = fasta_reference_db.index.region_for_entry(snp.contig).get_full_region
+    snp.full_sequence = fasta_reference_db.fetch_sequence(region)
+
+    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase)
+    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase)
+    assert_equal(snp.position, 101)
+    assert_equal(snp.original, "C")
+    assert_equal(snp.snp, "T")
+  end
+
+  def test_vcf_line
+    ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
+    
+    fasta_reference_db.load_fai_entries 
+    vcf="IWGSC_CSS_1AL_scaff_1455974	127	test_snp	C	T	135.03	.	"
+
+    chr_arm_parser = Bio::PolyploidTools::ChromosomeArm.getArmSelection("embl");
+    snp = Bio::PolyploidTools::SNP.parseVCF(vcf, chr_arm_parser: chr_arm_parser)
+    assert_equal(snp.gene , "test_snp", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size:  100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase, snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+
+    vcf="IWGSC_CSS_1AL_scaff_1455974\t127\ttest_snp\tC\tT\t135.03\t.\tOR=reverse"
+
+    chr_arm_parser = Bio::PolyploidTools::ChromosomeArm.getArmSelection("embl");
+    snp = Bio::PolyploidTools::SNP.parseVCF(vcf, chr_arm_parser: chr_arm_parser)
+    assert_equal(snp.gene , "test_snp", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size:  100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("TCTTGTACCTACCGAGTGCAGCATGCTACGTACCTTATAGCCAGAAGCCTTGACGTGGTGGATGCGGTCTCCAAAGCGCTTGTCAAGTCCGGGTACGACAA[G/A]GAGACCTGTAAGCAGCGCGTGCTCATACAGTCAGAGGACGCCCCGGTGCTTGCGGCGTTCAAGACGTTCCCCAAGTTCCAGCGGGTGCTGACGATCGAG", snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+
+  end
+
+  def test_reference_snp
+
+    ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
+    
+    fasta_reference_db.load_fai_entries 
+    
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1AL_scaff_1455974,C,127,T,1A")
+    assert_equal(snp.gene , "IWGSC_CSS_1AL_scaff_1455974", "The original name was not parsed: #{snp.gene}")
+    assert_equal("1A", snp.chromosome, "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(127, snp.position, "The position is not parsed: #{snp.position}")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga",     snp.template_sequence)
+    assert_equal("actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaag".upcase, snp.to_polymarker_sequence(100))
+    assert_equal(101,snp.position)
+    assert_equal("C",snp.original)
+    assert_equal("T",snp.snp)
+    
+    flanking_size = 3
+
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1DL_scaff_2258883,A,12498,C,1D")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: flanking_size)
+    assert_equal(4,snp.position)
+    assert_equal("A",snp.original)
+    assert_equal("C",snp.snp)
+    assert_equal("gatM", snp.template_sequence)
+
+    snp = Bio::PolyploidTools::SNP.parse("IWGSC_CSS_1BL_scaff_3810460,G,1,T,1B")
+    snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: flanking_size)
+    assert_equal(1,snp.position)
+    assert_equal("G",snp.original)
+    assert_equal("T",snp.snp)
+    assert_equal("Kaatt", snp.template_sequence)    
+  end
+
+  
+end

data/test/test_wrong_selection.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+test_out=$DIR/test_out
+rm -rf $test_out
+$DIR/../bin/polymarker.rb -c $DIR/data/PST130_7067.fa -s  $DIR/data/PST130_7067.csv -r $DIR/data/PST130_7067.fa  -o $test_out -e affine:local -a arm_selection_morex