[refactor] chimpanzee mitochondrion DNA test

orffinder/tests/gene.fasta

@@ -1,20 +1,238 @@
->NM_001115114.1 Danio rerio glyceraldehyde-3-phosphate dehydrogenase (gapdh), mRNA
-ACTCACACCAAGTGTCAGGACGAACAGAGGCTTCTCACAAACGAGGACACAACCAAATCAGGCATAATGG
-TTAAAGTTGGTATTAACGGATTCGGTCGCATTGGCCGTCTGGTGACCCGTGCTGCTTTCTTGACCAAGAA
-AGTGGAGATCGTGGCCATCAATGACCCATTCATTGACCTTGATTACATGGTTTACATGTTCCAGTACGAC
-TCCACCCATGGAAAGTACAAGGGTGAGGTTAAGGCAGAAGGCGGCAAACTGGTCATTGATGGTCATGCAA
-TCACAGTCTATAGCGAGAGGGACCCAGCCAACATTAAGTGGGGTGATGCAGGTGCTACTTATGTTGTGGA
-GTCTACTGGTGTCTTCACTACTATTGAGAAGGCTTCTGCTCACATTAAGGGTGGTGCAAAGAGAGTCATC
-ATCTCTGCCCCAAGTGCAGATGCCCCCATGTTTGTCATGGGTGTCAACCATGAGAAATATGACAACTCTC
-TCACAGTTGTAAGCAATGCCTCCTGCACCACCAACTGCCTGGCTCCTTTGGCAAAGGTCATCAATGATAA
-CTTTGTCATCGTTGAAGGTCTTATGAGCACTGTTCATGCCATCACAGCAACACAGAAGACCGTTGATGGG
-CCCTCTGGGAAGCTGTGGAGGGATGGCCGTGGTGCCAGTCAGAACATCATCCCAGCCTCCACTGGGGCTG
-CCAAGGCTGTAGGCAAAGTAATTCCTGAGCTCAATGGCAAGCTTACTGGTATGGCCTTCCGTGTCCCCAC
-CCCCAATGTCTCTGTTGTGGATCTGACAGTCCGTCTTGAGAAACCTGCCAAGTATGATGAGATCAAGAAA
-GTCGTCAAGGCTGCAGCTGATGGGCCCATGAAAGGAATTCTGGGATACACGGAGCACCAGGTTGTGTCCA
-CTGACTTCAATGGGGATTGCCGTTCATCCATCTTTGACGCTGGTGCTGGTATTGCTCTCAACGATCACTT
-TGTCAAGCTGGTCACATGGTATGACAATGAGTTCGGTTACAGCAACCGTGTATGTGACCTGATGGCACAC
-ATGGCCTCCAAGGAGTAGATGTGACCCCTTTGCTGTTTCTTTTTTTTGATACGCGACCATTCTCCCATCT
-GGTTGAATGTTTGCACCACGTGCCTGGAAGGAAATTACATGCTTAAATTGAAGACCAATATTATTTTTAT
-ATACTCTGTTCTGTTTCGTGTGTGAGGTTAAAAATAAATGTTGACTTCAAAGGCTTTTCTGTCTGTTAAC
-AACTTGCGATGGAATAAAAGTCCTCTGTTTGTGAGAAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+>NC_001643.1 Pan troglodytes mitochondrion, complete genome
+GTTTATGTAGCTTACCCCCTCAAAGCAATACACTGAAAATGTTTCGACGGGTTTACATCACCCCATAAAC
+AAACAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGCCCCGTG
+AGTCACCCTCTAAATCGCCATGATCAAAAGGAACAAGTATCAAGCACGCAGCAATGCAGCTCAAAACGCT
+TAGCCTAGCCACACCCCCACGGGAGACAGCAGTGATAAACCTTTAGCAATAAACGAAAGTTTAACTAAGC
+CATACTAACCTCAGGGTTGGTCAATTTCGTGCTAGCCACCGCGGTCATACGATTAACCCAAGTCAATAGA
+AACCGGCGTAAAGAGTGTTTTAGATCACCCCCCCATAAAGCTAAAATTCACCTGAGTTGTAAAAAACTCC
+AGCTGATACAAAATAAACTACGAAAGTGGCTTTAACACATCTGAATACACAATAGCTAAGACCCAAACTG
+GGATTAGATACCCCACTATGCTTAGCCCTAAACTTCAACAGTTAAATTAACAAAACTGCTCGCCAGAACA
+CTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGT
+AATCGATAAACCCCGATCAACCTCACCGCCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTG
+ATGAAGGTTACAAAGTAAGCACAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCTATGAGGTGGC
+AAGAAATGGGCTACATTTTCTACCCCAGAAAATTACGATAACCCTTATGAAACCTAAGGGTCAAAGGTGG
+ATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCA
+CCCTCCTCAAGTATACTTCAAAGGATACTTAACTTAAACCCCCTACGTATTTATATAGAGGAGATAAGTC
+GTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACATAAAGCACCCAAC
+TTACACTTAGGAGATTTCAACTCAACTTGACCACTCTGAGCCAAACCTAGCCCCAAACCCCCTCCACCCT
+ACTACCAAACAACCTTAACCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGTAAACCGGCGC
+AATAGACATAGTACCGCAAGGGAAAGATGAAAAATTATACCCAAGCATAATACAGCAAGGACTAACCCCT
+GTACCTTTTGCATAATGAATTAACTAGAAATAACTTTGCAAAGAGAACCAAAGCTAAGACCCCCGAAACC
+AGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAG
+GTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAA
+ATTTACCTACAGAACCCTCTAAATCCCCTTGTAAACTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTAG
+ACACTAGGAAAAAACCTTGTAAAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCA
+ATTAAGAAAGCGTTCAAGCTCAACACCCACAACCTTAAAGATCCCAAACATACAACCGAACTCCTTACAC
+CCAATTGGACCAATCTATTACCCCATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTC
+CGCATAAGCCTACATCAGACCAAAATATTAAACTGACAATTAACAGCCTAATATCTACAATCAACCAACA
+AGCCATTATTACCCCCGCTGTTAACCCAACACAGGCATGCCCACAAGGAAAGGTTAAAAAAAGTAAAAGG
+AACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATTACCAGTATTAGAGGCACC
+GCCTGCCCGGTGACATATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATAATCACTTGTTC
+CTTAAATAGGGACTTGTATGAATGGCTCCACGAGGGTTTAGCTGTCTCTTACTTTCAACCAGTGAAATTG
+ACCTACCCGTGAAGAGGCGGGCATAACATAACAAGACGAGAAGACCCTATGGAGCTTTAATTCATTAATG
+CAAACAATACTTAACAAACCTACAGGTCCTAAACTATTAAACCTGCATTAAAAATTTCGGTTGGGGCGAC
+CTCGGAGCACAACCCAACCTCCGAGCAATACATGCTAAGACCTCACCAGTCAAAGCGAATTACTACATCC
+AATTGATCCAATGACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCCAGAGTC
+CATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAG
+GTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTA
+TCTGTTCTAAATTTCTCCCTGTACGAAAGGACAAGAGAAATGAGGCCTACTTCACAAAGCGCCTTCCCCA
+ATAAATGATATTATCTCAATTTAGCGCCATGCCAACACCCACTCAAGAACAGAGTTTGTTAAGATGGCAG
+AGCCCGGTAATTGCATAAAACTTAAAACTTTACAATCAGAGGTTCAATTCCTCTTCTTGACAACACACCC
+ATGACCAACCTCCTACTCCTCATTGTACCCATCCTAATCGCAATAGCATTCCTAATGCTAACCGAACGAA
+AAATTCTAGGCTACATACAACTACGCAAAGGTCCCAACATTGTAGGTCCTTACGGGCTATTACAGCCCTT
+CGCTGACGCCATAAAACTCTTCACTAAAGAACCCTTAAAACCCTCCACTTCAACCATTACCCTCTACATC
+ACCGCCCCAACCCTAGCCCTCACCATTGCCCTCTTACTATGAACCCCCCTCCCCATACCCAACCCCCTAG
+TCAATCTTAACTTAGGCCTCCTATTTATTCTAGCCACCTCCAGCCTAGCCGTTTACTCAATCCTCTGATC
+AGGGTGAGCATCAAACTCGAACTACGCCTTAATCGGTGCACTACGAGCAGTAGCCCAAACAATCTCATAC
+GAAGTCACTCTAGCCATTATCCTACTGTCAACGCTACTAATAAGTGGCTCCTTCAATCTCTCTACCCTTG
+TCACAACACAAGAGCACCTCTGACTAATCCTGCCAACATGACCCCTGGCCATAATATGATTTATCTCTAC
+ACTAGCAGAGACCAACCGAACTCCCTTCGACCTTACTGAAGGAGAATCTGAACTAGTCTCAGGCTTTAAT
+ATCGAGTATGCCGCAGGCCCCTTTGCCCTATTTTTCATAGCCGAATACATAAACATTATTATAATAAACA
+CCCTCACTGCTACAATCTTCCTAGGAGCAACATACAATACTCACTCCCCTGAACTCTACACGACATATTT
+TGTCACCAAAGCTCTACTTCTAACCTCCCTGTTCCTATGAATTCGAACAGCATATCCCCGATTTCGCTAC
+GACCAGCTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATCACTCATGTGATATATCT
+CCATACCCACTACAATCTCCAGCATCCCCCCTCAAACCTAAGAAATATGTCTGATAAAAGAATTACTTTG
+ATAGAGTAAATAATAGGAGTTCAAATCCCCTTATTTCTAGGACTATAAGAATCGAACTCATCCCTGAGAA
+TCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTCAGCTAAATAAGCTATCGGGCCC
+ATACCCCGAAAATGTTGGTTACACCCTTCCCGTACTAATTAATCCCCTAGCCCAACCCATCATCTACTCT
+ACCATCCTTACAGGCACGCTCATTACAGCGCTAAGCTCACACTGATTTTTCACCTGAGTAGGCCTAGAAA
+TAAATATACTAGCTTTTATCCCAATCCTAACCAAAAAAATAAGCCCCCGCTCCACAGAAGCCGCCATCAA
+ATACTTTCTCACACAAGCAACTGCGTCCATAATTCTCCTGATAGCTATCCTCTCCAACAGCATACTCTCC
+GGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATAATTATAATAGCAATGGCAATAA
+AACTAGGAATAGCCCCCTTTCACTTTTGAGTTCCAGAAGTTACCCAAGGCACCCCCCTAATATCCGGCCT
+ACTCCTCCTCACATGACAAAAATTAGCCCCTATTTCAATTATATACCAAATCTCCTCATCACTGAACGTA
+AACCTTCTCCTCACCCTTTCAATCTTGTCCATTATAGCAGGCAGCTGAGGCGGACTAAACCAAACCCAAC
+TACGCAAAATCCTAGCATACTCCTCAATCACCCACATAGGCTGAATAATAGCAGTCCTACCATATAACCC
+TAACATAACCATTCTTAATTTAACCATTTACATCATCCTAACTACTACCGCATTTCTGCTACTCAACTTA
+AACTCCAGCACCACAACCCTACTACTATCTCGCACCTGAAACAAGCTAACATGATTAACTCCCCTAATTC
+CATCCACCCTCCTCTCCCTAGGAGGCCTACCCCCACTAACTGGCTTCTTACCCAAATGAGTTATCATCGA
+AGAATTCACAAAAAATAATAGCCTCATCATCCCCACCATCATAGCCATCATCACTCTCCTTAACCTCTAT
+TTCTACCTACGCCTAATCTACTCCACCTCAATTACACTACTTCCCATATCTAATAACGTAAAAATAAAAT
+GACAATTCGAACATACAAAACCCACCCCCTTCCTCCCTACACTCATCACCCTTACCACACTGCTTCTACC
+CATCTCCCCCTTCATACTAATAATCTTATAGAAATTTAGGTTAAGCACAGACCAAGAGCCTTCAAAGCCC
+TCAGCAAGTTACAATACTTAATTTCTGCAACAACTAAGGACTGCAAAACCCCACTCTGCATCAACTGAAC
+GCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGATTAATGGGACTTAAACCCACAAACATTTAGT
+TAACAGCTAAACACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCAAGAAAAAAAGGCGGGAGAA
+GCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCAGAGCTGGTAAA
+AAGAGGCTTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCCCACCCTACTG
+ATGTTCACCGACCGCTGACTATTCTCTACAAACCACAAAGATATTGGAACACTATACCTACTATTCGGTG
+CATGAGCTGGAGTCCTGGGCACAGCCCTAAGTCTCCTTATTCGGGCTGAACTAGGCCAACCAGGCAACCT
+CCTAGGTAATGACCACATCTACAATGTCATCGTCACAGCCCATGCATTCGTAATAATCTTCTTCATAGTA
+ATGCCTATTATAATCGGAGGCTTTGGCAACTGGCTAGTTCCCTTGATAATTGGTGCCCCCGACATGGCAT
+TCCCCCGCATAAACAACATAAGCTTCTGGCTCCTGCCCCCTTCTCTCCTACTTCTACTTGCATCTGCCAT
+AGTAGAAGCCGGCGCGGGAACAGGTTGAACAGTCTACCCTCCCTTAGCGGGAAACTACTCGCATCCTGGA
+GCCTCCGTAGACCTAACCATCTTCTCCTTACATCTGGCAGGCATCTCCTCTATCCTAGGAGCCATTAACT
+TCATCACAACAATTATTAATATAAAACCTCCTGCCATGACCCAATACCAAACACCCCTCTTCGTCTGATC
+CGTCCTAATCACAGCAGTCTTACTTCTCCTATCCCTCCCAGTCCTAGCTGCTGGCATCACCATACTATTG
+ACAGATCGTAACCTCAACACTACCTTCTTCGACCCAGCCGGGGGAGGAGACCCTATTCTATATCAACACT
+TATTCTGATTTTTTGGCCACCCCGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATTTCCCACAT
+TGTAACTTATTACTCCGGAAAAAAAGAACCATTTGGATATATAGGCATGGTTTGAGCTATAATATCAATT
+GGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGGATAGACGTAGACACCCGAGCCT
+ATTTCACCTCCGCTACCATAATCATTGCTATTCCTACCGGCGTCAAAGTATTCAGCTGACTCGCTACACT
+TCACGGAAGCAATATGAAATGATCTGCCGCAGTACTCTGAGCCCTAGGGTTTATCTTTCTCTTCACCGTA
+GGTGGCCTAACCGGCATTGTACTAGCAAACTCATCATTAGACATCGTGCTACACGACACATACTACGTCG
+TAGCCCACTTCCACTACGTTCTATCAATAGGAGCTGTATTCGCCATCATAGGAGGCTTCATTCACTGATT
+CCCCCTATTCTCAGGCTATACCCTAGACCAAACCTATGCCAAAATCCAATTTGCCATCATGTTCATTGGC
+GTAAACCTAACCTTCTTCCCACAGCACTTCCTTGGCCTATCTGGGATGCCCCGACGTTACTCGGACTACC
+CCGATGCATACACCACATGAAATGTCCTATCATCCGTAGGCTCATTTATCTCCCTGACAGCAGTAATATT
+AATAATTTTCATGATTTGAGAAGCCTTTGCTTCAAAACGAAAAGTCCTAATAGTAGAAGAGCCCTCCGCA
+AACCTGGAATGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTA
+GACAAAAAAGGAAGGAATCGAACCCCCTAAAGCTGGTTTCAAGCCAACCCCATGACCTCCATGACTTTTT
+CAAAAAGATATTAGAAAAACTATTTCATAACTTTGTCAAAGTTAAATTACAGGTTAACCCCCGTATATCT
+TAATGGCACATGCAGCGCAAGTAGGTCTACAAGATGCTACTTCCCCTATCATAGAAGAACTTATTATCTT
+TCACGACCATGCCCTCATAATTATCTTTCTCATCTGCTTTCTAGTCCTATACGCCCTTTTCCTAACACTC
+ACAACAAAACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCG
+CCATCATCCTAGTCCTTATTGCCCTACCATCCCTGCGTATCCTTTACATAACAGACGAGGTCAACGACCC
+CTCCTTTACTATTAAATCAATCGGCCATCAATGATATTGAACCTACGAATACACCGACTACGGCGGGCTA
+ATCTTCAACTCCTACATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATA
+ACCGAGTGGTCCTCCCAGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATG
+AGCTGTTCCCACATTAGGCCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCC
+ACACGACCAGGAGTATACTACGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCG
+TCCTAGAATTAATCCCTCTAAAAATCTTTGAAATAGGACCCGTATTCACTCTATAGCACCTTCTCTACCC
+CTCTCCAGAGCTCACTGTAAAGCTAACCTAGCATTAACCTTTTAAGTTAAAGATTAAGAGGACCGACACC
+TCTTTACAGTGAAATGCCCCAACTAAATACCGCCGTATGACCCACCATAATTACCCCCATACTCCTGACA
+CTATTTCTCGTCACCCAACTAAAAATATTAAATTCAAATTACCATCTACCCCCCTCACCAAAACCCATAA
+AAATAAAAAACTACAATAAACCCTGAGAACCAAAATGAACGAAAATCTATTCGCTTCATTCGCTGCCCCC
+ACAATCCTAGGCTTACCCGCCGCAGTACTAATCATTCTATTCCCCCCTCTACTGGTCCCCACTTCTAAAC
+ATCTCATCAACAACCGACTAATTACCACCCAACAATGACTAATTCAACTGACCTCAAAACAAATAATAAC
+TATACACAGCACTAAAGGACGAACCTGATCTCTCATACTAGTATCCTTAATCATTTTTATTACCACAACC
+AATCTTCTTGGGCTTCTACCCCACTCATTCACACCAACCACCCAACTATCTATAAACCTAGCCATGGCTA
+TCCCCCTATGAGCAGGCGCAGTAGTCATAGGCTTTCGCTTTAAGACTAAAAATGCCCTAGCCCACTTCTT
+ACCGCAAGGCACACCTACACCCCTTATCCCCATACTAGTTATCATCGAAACTATTAGCCTACTCATTCAA
+CCAATAGCCTTAGCCGTACGTCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAA
+GCGCCACACTAGCATTATCAACTATCAATCTACCCTATGCACTCATTATCTTCACAATTCTAATCCTACT
+GACTATTCTAGAGATCGCCGTCGCCTTAATCCAAGCCTACGTTTTTACACTTCTAGTGAGCCTCTACCTG
+CACGACAACACATAATGACCCACCAATCACATGCCTACCACATAGTAAAACCCAGCCCATGACCCCTAAC
+AGGGGCCCTCTCGGCCCTCCTAATAACCTCCGGCCTGGCCATATGATTCCACTTCTACTCCACAACACTA
+CTCACACTAGGCTTACTAACTAACACATTGACCATATATCAATGATGACGCGATGTTATACGAGAAGGCA
+CATACCAAGGCCACCACACACCACCCGTCCAAAAAGGTCTCCGATATGGGATAATTCTTTTTATTACCTC
+AGAAGTTTTTTTCTTTGCAGGATTTTTTTGAGCTTTCTACCACTCCAGCCTAGCCCCTACCCCCCAGCTA
+GGAGGACACTGGCCCCCAACAGGTATTACCCCACTAAATCCCCTAGAAGTCCCACTCCTAAACACATCTG
+TATTACTCGCATCAGGAGTATCAATTACTTGAGCCCATCACAGCTTAATAGAAAATAACCGAAACCAAAT
+AATTCAAGCACTGCTTATTACGATTCTACTAGGTCTTTATTTTACCCTCCTACAAGCCTCAGAATATTTC
+GAATCCCCTTTTACCATTTCCGATGGCATCTACGGCTCAACATTCTTTGTAGCCACAGGCTTCCACGGAC
+TCCACGTCATTATTGGATCAACTTTCCTCACTATCTGCCTCATCCGCCAACTAATATTTCACTTCACATC
+CAAACATCACTTCGGCTTTCAAGCCGCCGCCTGATACTGACACTTCGTAGATGTAGTCTGACTATTTCTA
+TATGTCTCTATTTACTGATGAGGATCTTACTCTTTTAGTATAAGTAGTACCGTTAACTTCCAATTAACTA
+GTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGTCCTAATTTTAATAACCAATACCCTTCTAGCCCT
+ACTACTGATAATTATCACATTCTGACTACCACAACTCAACAGCTACATAGAAAAATCTACCCCTTACGAA
+TGTGGCTTCGACCCTATATCCCCCGCCCGCGTCCCCTTCTCCATAAAATTTTTCCTAGTAGCCATCACCT
+TCCTATTATTTGACCTAGAAATTGCCCTCCTATTGCCCTTACCTTGAGCCCTACAAACGGCCAACCTACC
+ACTAATAGTCACATCATCCCTCTTATTAATTACTATCCTAGCCCTAAGCCTCGCCTACGAATGATTACAA
+AAAGGGTTAGACTGAACCGAATTGGTATATAGTTTAAATAAAACGAATGATTTCGACTCATTAAATTATG
+ATAATCATATTTACCAAATGCCCCTTATTTATATAAATATTATACTAGCATTTACCATCTCACTTCTAGG
+AATACTAGTATATCGCTCACACCTAATATCTTCCCTACTATGCCTAGAAGGAATAATACTATCACTGTTC
+ATCATAGCCACCCTCATAACCCTCAATACTCACTCCCTCTTAGCCAATATTGTACCCATCACCATACTAG
+TCTTTGCTGCCTGCGAAGCAGCAGTAGGTCTAGCACTACTAGTTTCAATCTCTAACACATATGGCTTAGA
+CTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCATCCCGACAATTATATTACTACCACTAA
+CATGATTCTCTAAAAAACGTATAATTTGAATCAACACAACCACTCACAGCCTAATTATCAGCACCATTCC
+CTTACTATTTTTTAACCAAATTAACAACAACCTATTCAGCTGTTCCCTGCCCTTCTCCTCCGACCCCTTA
+ACAACTCCCCTCCTAATATTAACTGCTTGACTTCTACCCCTCACAATCATAGCAAGCCAGCGCCACCTAT
+CCAACGAACCACTATCACGAAAAAAACTCTACCTCTCCATGCTAATTTCCCTCCAAATCTCCTTAATTAT
+AACATTCTCGGCCACAGAGCTAATTATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCCTGGCT
+ATCATCACCCGATGGGGTAACCAACCAGAACGCCTGAACGCAGGTACATACTTCCTATTCTATACCCTAG
+TAGGCTCCCTCCCCCTACTCATCGCACTAATCTATACCCACAACACCCTAGGCTCACTAAATATCCTATT
+ACTCACTCTTACAACCCAAGAACTATCAAACACCTGAGCCAACAACTTAATATGACTAGCGTACACGATG
+GCTTTCATGGTAAAAATACCCCTTTACGGACTCCACCTATGACTCCCTAAAGCCCATGTCGAAGCCCCTA
+TTGCCGGGTCAATGGTACTTGCTGCAGTACTCTTAAAATTAGGTGGCTATGGCATAATACGCCTCACACT
+CATCCTCAACCCCCTAACAAAACATATAGCCTATCCCTTCCTCATGTTGTCCTTATGAGGTATAATCATA
+ACAAGCTCCATCTGCCTGCGACAAACAGACCTAAAATCGCTCATTGCATACCCTTCAGTCAGCCACATAG
+CCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAATTATCCTCATAATCGC
+CCACGGACTTACATCCTCATTATTATCCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATC
+ATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTGGCAAGCCTCG
+CTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTG
+ATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTT
+ACCACAACACAATGAGGCTCACTCACCCACCACATTAATAGCATAAAGCCCTCATTCACACGAGAAAACA
+CTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCAC
+CTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCACGACCCCTTATT
+TACCGAGAAAGCTTATAAGAACTGCTAACTCGTATTCCCATGCCTAACAACATGGCTTTCTCAACTTTTA
+AAGGATAACAGTTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACC
+ATGTATGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCCATCCTCGGCGCCCTCATTAACC
+CTAACAAAAAAAACTCATACCCCCATTACGTGAAATCCATTATCGCATCCACCTTTATCATTAGCCTTTT
+CCCCACAACAATATTCATATGCCTAGACCAAGAAACTATTATCTCGAACTGACACTGAGCAACAACCCAA
+ACAACCCAACTCTCCCTGAGCTTTAAACTAGACTATTTCTCCATAACATTTATCCCCGTAGCACTGTTCG
+TTACATGATCCATCATAGAATTCTCACTATGATATATAGACTCAGACCCCAACATCAACCAATTCTTCAA
+ATACTTACTTATCTTCCTAATTACTATACTAATCCTAGTCACCGCTAACAACCTATTCCAACTCTTCATC
+GGCTGAGAAGGCGTAGGAATTATATCCTTTCTACTCATTAGCTGATGGTACGCCCGAACAGATGCCAACA
+CAGCAGCCATCCAAGCAATCCTATATAACCGTATCGGTGATATTGGTTTTGTCCTAGCCCTAGCATGATT
+TCTCCTACACTCCAACTCATGAGATCCACAACAAATAATCCTCCTAAGTACTAATACAGACCTTACTCCA
+CTACTAGGCTTCCTCCTAGCAGCAGCAGGCAAATCAGCTCAACTAGGCCTTCACCCCTGACTCCCCTCAG
+CCATAGAAGGCCCTACCCCTGTTTCAGCCCTACTCCACTCAAGCACCATAGTCGTAGCAGGAATCTTCCT
+ACTCATCCGCTTCTACCCCCTAGCAGAGAATAACCCACTAATCCAAACTCTCACGCTATGCCTAGGCGCT
+ATCACCACCCTATTCGCAGCAGTCTGCGCCCTCACACAAAATGACATCAAAAAAATCGTGGCCTTCTCCA
+CTTCAAGCCAACTAGGACTCATAATAGTTACAATCGGTATCAACCAACCACACCTAGCATTCCTTCACAT
+CTGCACCCACGCTTTCTTCAAAGCCATACTATTCATATGCTCCGGATCCATTATTCACAACCTCAATAAT
+GAGCAAGACATTCGAAAAATAGGAGGATTACTCAAAACCATACCCCTCACTTCAACCTCCCTCACCATTG
+GGAGCCTAGCATTAGCAGGAATACCCTTCCTCACAGGTTTCTACTCCAAAGACCTCATCATCGAAACCGC
+TAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCCACCTCTCTGACAAGCGCCTAC
+AGCACCCGAATAATCCTCCTCACCCTAACAGGTCAACCTCGCTTCCCAACCCTCACCAACATTAACGAAA
+ACAACCCCACTCTGTTAAATCCCATTAAACGCCTAACCATTGGAAGCTTATTTGCAGGATTTCTCATTAC
+CAACAACATTCTCCCCATATCTACTCCCCAAGTGACAATTCCCCTTTACTTAAAACTTACAGCCCTAGGC
+GTTACTTCCCTAGGACTTCTAACAGCCCTAGACCTCAATTACCTAACCAGCAAGCTCAAAATAAAATCCC
+CACTATATACATTTCACTTCTCTAATATACTCGGATTCTACCCTAACATTATACACCGCTCGATCCCCTA
+TCTAGGCCTTCTTACAAGCCAAAACCTACCCCTACTTCTTCTAGACCTGACCTGACTAGAGAAACTATTA
+CCTAAAACAATTTCACAGTACCAAATCTCCGCTTCCATTACCACCTCAACCCAAAAAGGCATGATCAAAC
+TTTATTTCCTCTCTTTTTTCTTCCCTCTCATCTTAACCTTACTCCTAATCACATAACCTATTCCCCCGAG
+CAATCTCAATCACAATGTATACACCAACAAACAATGTCCAACCAGTAACTACTACTAACCAACGCCCATA
+ATCATATAAGGCCCCCGCACCAATAGGATCCTCCCGAATCAGCCCTGGCCCCTCCCCTTCATAAATTATT
+CAACTTCCCACGCTATTAAAATTTACCACAACCACCATCCCATCATACCCTTTTACCCATAACACTAATC
+CTACCTCCATCGCCAGTCCTACTAAAACACTAACCAAAACCTCAACCCCTGACCCCCATGCCTCAGGATA
+CTCCTCAATAGCCATAGCCGTAGTATACCCAAAAACAACCATTATTCCCCCCAAATAAATTAAAAAAACC
+ATTAAACCTATATAACCTCCCCCATAATTCAAAATGATGGCACACCCAACTACACCACTAACAATCAATA
+CTAAACCCCCATAAATGGGAGAAGGCTTAGAAGAAAACCCCACAAACCCTATCACTAAACTCACACTCAA
+TAAAAATAAAGCATATGTCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGT
+TGTATTTCAACTACAAGAACACCAATGACCCCGACACGCAAAATTAACCCACTAATAAAATTAATTAATC
+ACTCATTTATCGACCTCCCCACCCCATCCAACATTTCCGCATGATGGAACTTCGGCTCACTTCTCGGCGC
+CTGCCTAATCCTTCAAATTACCACAGGATTATTCCTAGCTATACACTACTCACCAGACGCCTCAACCGCC
+TTCTCGTCGATCGCCCACATCACCCGAGACGTAAACTATGGTTGGATCATCCGCTACCTCCACGCTAACG
+GCGCCTCAATATTTTTTATCTGCCTCTTCCTACACATCGGCCGAGGTCTATATTACGGCTCATTTCTCTA
+CCTAGAAACCTGAAACATTGGCATTATCCTCTTGCTCACAACCATAGCAACAGCCTTTATGGGCTATGTC
+CTCCCATGAGGCCAAATATCCTTCTGAGGAGCCACAGTAATTACAAACCTACTGTCCGCTATCCCATACA
+TCGGAACAGACCTGGTCCAGTGAGTCTGAGGAGGCTACTCAGTAGACAGCCCTACCCTTACACGATTCTT
+CACCTTCCACTTTATCTTACCCTTCATCATCACAGCCCTAACAACACTTCATCTCCTATTCTTACACGAA
+ACAGGATCAAATAACCCCCTAGGAATCACCTCCCACTCCGACAAAATTACCTTCCACCCCTACTACACAA
+TCAAAGATATCCTTGGCTTATTCCTTTTCCTCCTTATCCTAATGACATTAACACTATTCTCACCAGGCCT
+CCTAGGCGATCCAGACAACTATACCCTAGCTAACCCCCTAAACACCCCACCCCACATTAAACCCGAGTGA
+TACTTTCTATTTGCCTACACAATCCTCCGATCCATCCCCAACAAACTAGGAGGCGTCCTCGCCCTACTAC
+TATCTATCCTAATCCTAACAGCAATCCCTGTCCTCCACACATCCAAACAACAAAGCATAATATTTCGCCC
+ACTAAGCCAACTGCTTTACTGACTCCTAGCCACAGACCTCCTCATCCTAACCTGAATCGGAGGACAACCA
+GTAAGCTACCCCTTCATCACCATCGGACAAATAGCATCCGTATTATACTTCACAACAATCCTAATCCTAA
+TACCAATCGCCTCTCTAATCGAAAACAAAATACTTGAATGAACCTGCCCTTGTAGTATAAACTAATACAC
+CGGTCTTGTAAACCGGAAACGAAAACTTTCTTCCAAGGACAAATCAGAGAAAAAGTAATTAACTTCACCA
+TCAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAAATTTAGGTAC
+CACCTAAGTACTGGCTCATTCATTACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATAT
+CGTACAGTACCATATCACCCAACTACCTATAGTACATAAAATCCACTCCCACATCAAAACCTTCACTCCA
+TGCTTACAAGCACGCACAACAATCAACTCCCAACTGTCGAACATAAAACACAATTCCAACGACACCCCTC
+CCCCACCCCGATACCAACAGACCTATCTCCCCTTGACAGAACATAGTACATACAACCATACACCGTACAT
+AGCACATTACAGTCAAACCCCTCCTCGCCCCCACGGATGCTCCCCCTCAGATAGGAATCCCTTGGTCACC
+ATCCTCCGTGAAATCAATATCCCGCACAAGAGTGACTCTCCTCGCTCCGGGCCCATAACATCTGGGGGTA
+GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACCTCAGGGCCATGAAGTTCAAAAGACTCCCACACGT
+TCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCAGTCACGGGAGCCTTCCA
+TGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAAACGCTGGCCCCGGAGCACCCT
+ATGTCGCAGTATCTGTCTTTGATTCCTGCCCCATTGTATTATTTATCGCACCTACGTTCAATATTACGAC
+CTAGCATACCTACTAAAGTGTGTTGATTAATTAATGCTTGCAGGACATAACAACAGCAGCAAAATGCTCA
+CATAACTGCTTTCCACACCAACATCATAACAAAAAATTCCCACAAACCCCCCCTTCCCCCCGGCCACAGC
+ACTCAAACAAATCTCTGCCAAACCCCAAAAACAAAGAACCCAGACGCCAGCCTAGCCAGACTTCAAATTT
+CATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCTCAATTAACATGCCCTCCCCCCTCAACTCCCATT
+CTACTAGCCCCAGCAACGTAACCCCCTACTCACCCTACTCAACACATATACCGCTGCTAACCCCATACCC
+TGAACCAACCAAACCCCAAAGACACCCCTACACA

orffinder/tests/test.py

@@ -3,7 +3,26 @@
 
 import orffinder
 
-sequence = list(SeqIO.parse("gene.fasta", "fasta"))[0]
+sequence = list(SeqIO.parse("tests/gene.fasta", "fasta"))[0]
 
-out = orffinder.getORFProteins(sequence, minimum_length=75, remove_nested=True)
-print(out)
+out = orffinder.getORFProteins(sequence, return_loci=True, minimum_length=75, remove_nested=False, trim_trailing=False)
+
+for orf in out:
+
+    start = min(orf["start"], orf["end"])
+    end = max(orf["start"], orf["end"])
+    length = end - start
+
+    print(orf["sense"])
+
+    if orf["sense"] == "+":
+
+        print(sequence.seq[start - 1 : end - 1])
+
+    else:
+        print(sequence.seq[start - 1 : end - 1])
+
+    print(orf["protein"])
+    print("\n")
+
+print(len(out))