--- /dev/null
+##gff-version 2
+##source-version exonerate:cdna2genome 2.4.0
+##date 2021-02-03
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+CDS|ENST00000398721/1-183 exonerate:cdna2genome similarity 1 183 885 + . alignment_id 0 ; Target ENSG00000214643/1-4245 ; Align 1 822 59 ; Align 60 4039 124
+##FASTA
+>ENSG00000214643/1-4245 chromosome:GRCh38:6:49946021:49950265:-1
+CTCCTGCCTCAGCCTCTGGGAGTAGCTGGGACTACAGGGGCCCGCCACCACGCCCGGATAATTTTTTTCTAT
+TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCGGGACGGTCTTAATCTCCTGACCTAGTTATCCGCCAGC
+CTCGGCCTCCCAAAGTGCTGGAATTACGGGTGTGAGTATATTGCTTTTTAAATTCACTAGTTTATTCATTAT
+GTATAGCTATTTAAAAAAGAGAAAAACTGTCCTGGCTAACACGGTGAAACCCCGTTTCTACTAAAAATACAA
+AAAATTAGCCGGCCTGGTGGCGGGTGCCTGTAGTACCACCTACTCTGGAGGCTGAGGCAGGAGAATGGCGTG
+AACCCGGGAGGCAGAGCTTGCAGTGAGTCGCGATCGCGCCACTGAACTCCAGCCTGGGTGACAGAACGAGAC
+TCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGAAACTAAATCAAAAG
+CAAAGATTAAATTCTCATGCTTCTACTTTTCAGACCTTCAATAGGAGATTCTCAGTGGCATGCACTTCCTAG
+ACAACCAGTTATTAAAAAGATAATTATATACTATGGATATCATAACCCTTTATATCCCAAGATAAAAGAAAA
+GTAATGTCCTGCATTTTTGCCCCAGGCACTGCTAAACAGGAGTGTTAACTTTTGATAAACCCCAGTTTCTAA
+ATTCGTACAACTGCATGGAGAGAAGTATAAAAAGATGTGCTCTCCACCTTTCTCTTATTCAAACACTGCAGA
+GCTGCTAATTCGGCTGACTGTCTTCAATCATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGG
+TCCCCATTGCCACCAGGTAAAATGTAAATATTGAGAGGGTAAAATATCTTTCTGGAGAGTTGCATTTTGGTC
+GATGTCAACTGGAGACACAAGAGTGACCAGATTGTTAAGAGAGTGGTTGGTTACGGTCCCAAGAGTAAATCA
+CAAATAAAGGACTGTGGTCTTACTAAACAGTAAGGCTCCGGGTGAGTCATATTATTGTATGAGACAATTTAA
+AGGCCTTGATTAAATGACTACAGGCTGGTTGTCCAGACTGACTACTTGGATAGAATATTAAAGTATAACCAT
+CTGGATCCTTGAGACATTGATGGGCACTGTGTAGTAGAGTAACAGTTGGTTTTTCAGTAACCTCATGATAGG
+TTTGGTTATATTATGTCACAAGGTTTACTTTGAGAAAAACACAAAATGGTGTTTTCAACTGATTAAGAATTG
+AGAACTTCAGTGGCTGTATTACCTCAGGTCCAATTACATAGCAATTAATACTAACCAGATAATTAAATGAGT
+ATAAACTTTGGAATAATTGATACCTGGGTTCAGATTTGGCTTTTGCCATGTATTGGCTATGCAAATCTATCA
+GGTTATTTACACTCATTCAGCATCAATTTCCTCATTTGCGAATTAAATACAGTAATTAAGTCTATCTGTAGT
+ATTATGACGATTAATGATATTTAAATATACAAAATGCCCAACATAAAGTATAATACACATCAGATTCATCTT
+AAATAGTATTATAATTACTTTTACATTGTATTAAAACACCTTAAAAAGCAAGTAACATCTAGAAATCTCATC
+GAGAAACTCTTTCTTGACAACTATTGCAGGAAACAGGGGAGGTAATATTTACCATGTTGGATTTCACATACT
+TAAACTGTGTACCCTCATTTGTAAACTTTCATTGTACACACTACTATTAGATTAGATCAATAGCCAAAGGAA
+GTATCTTGATGGAGATCATCGAAAGAGCTGTTTTAACACATTTCAGGGTACTTATGATAGGAAAAGTATTTT
+TCTTATTTATGTAAAGACCCTGTAAACAATCATTTTACACACACCCAAGAAAATAATTCCACTCACCTTAAG
+AAAATAAAACAAACAAAAAAATAATAACTATAGGGCATTCTGATTTAGGAGTGGTCTAGAACTGCAAGAGTT
+TCCTCTTTGAAGTCCAACTTCATTCCTTAGCAGCACAGATGAGACCAAGGAAGTCTAGCTCTAACAATAAGT
+CTGGCTGTGAGTAAACTCAAACATCTAAGTATTTTGGATAAAAGACTCAAATCATTTTAATTGTTTTATAAT
+TCAAGTAAAATATGTCAGATGATAATTTTGAGGATTGTTATTTTATTACATCATTCTAAACTCAAGACTAAT
+GGAATTACAATCAGGGTTTGTTTTTACTAAAACCATATGGGGGTGATCTTAAAATAAAGAAGACTTATTTAG
+TGCAACCACATTTGGATAATAAAATTAGCTCCAGTTATGTTATCATGATTTACATGTGTGCCTCATGTCACT
+TGCTTTGGGAAAAAAGGTGAAAATTTTCATGACATTTTCAGTTTCATTATAAACCCAAGAGACATTATGAAT
+GTATGTGCATAGATTCATCTAAAAATTGAGAAATTTGTGATTCCTTCTTGTACATAAATAAATTTTTATGTT
+ATACATAGCTGTTATCTAGAGAGAAGCTGTTTGTTGTTTTTGTTACTAGTGGAAAAATGCTAATTTACAATT
+CCCACTTAAATAATGCTATTCTTTTTTTAATACTAGTGTTTGACAGCTGTCATCTTCTATTATTTGTAAATT
+CCAATTAAGTCAACATACATGCTTCACACCCATCATGTAGGACAGTGTAATCTGAGGATGCATTTTTAAGCT
+GGCAAGATAATGCTTTTTCCCTCTGGCATCAAAGGCAATAAATAGCATCTCTCTAGATAATACAAATAAAGA
+GATATCTATCATTAATTTATACAGTGAAAAAGCATATCTCGTTGCCTAAAATATTTGGCAAAAAATTCAAAA
+TAATATGTTCAATTTTTTCCTAAAATGTCTAGTTACTCCAAGTAACAGTAAGACTGTATGCTAACATAACTT
+CACTGAAAGCAGATGACATGAATTGGGTTATCAGTACCTTTGACTCCATCTCAGTTGGATCCTATATGTTGA
+GCACCTAGAGAAAGAGCACCTTTCACATACCTTTGTCACTGATATTTGATAATTTACCATTACATTTAATGC
+TTTAACTTTGGGCGTCTTCCTCCTTATGTGACCTTTCTAAAAATTTAAACATTTTGTGAAGAGATGAAACAT
+TAAGTCTTATGGCCAGATGTAGATGAGTTCATCAGCTGGTATATGCTATGATGATGCAATCCTGAGAACTTT
+ATAAAGGAGAAGACTCTGAAACAAGGAAACATACGGAGATGCTGAGAGATACTACCTCTTTCTCTTTGAACT
+TAAGGCTTGTCATTCATGACAACACTCATCCCCCCAGCAAACCAGGCTCCTGCCTAGGCTCAAATCTTTGTG
+AATATTCAAAGAACCTCTCTTATCCCAGTATCTGCTAGGGTTTTTTTCACTCTTCTAATAAAAGAGATTTAT
+AAAAAATATTCGAGCAAGATAGCAATTGAAGCAACATTAATGAATCTTCCCATTTTAAATCCTGAAACCAAA
+AATGTTTAAATGTTTAATTTTTTTTTTGAAATTGGAGAAAAAAGCCTTTGGGAGGTGATGGGATCATAGATA
+TTTGTATATGCCCAAATTCATCATTTGTACACATTAAATATGTGCAGTTCTTTTTATAGCAACTATACCTCA
+ATAAAGTTGTTTTTTTAAAAAAATCATGTTAGGTGGGTAGTAGGTAAGTAGCCATAGAAATATGTGGTGTTC
+ATTCCAGAACTACTTGAAATCTAACAATTTTTATTTAGAAATTCTCAGGGAAAACTAAGCTTTAACAACTAG
+TGGATCAAGCCAGAAGTTGGAGAGGAAACTGAGAATGAAACAGAAAGTATCACAGAACAATCATCACCAGAA
+AAATACAAAACAAATGACTTCCCAAATCCCTACCCCAGAATGCAAGGGCTATACTTATTTTCACATTGACAA
+CTGATTTATCCCAAGGTGGGACCTTAAGACACTTATAGTGACTCAATGGTTTATGTGCTTTCTTTTTCCCCT
+TTTAACAGTGAAATGTGCCGTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTG
+TCATGATTTTGAAAAACCAATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATGTAGAAGTTTGAAAT
+AAAAATCAGCATCCCTCAAAAGTAAAGCACAGTGAGTACAAGGATTAGTAATAAAAGAAACTGAATTAC
+>CDS|ENST00000398721/1-183 DEFB133-201
+ATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGGTCCCCATTGCCACCAGGGTGAAATGTGCC
+GTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTGTCATGATTTTGAAAAACCA
+ATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATG
--- /dev/null
+##gff-version 2
+##source-version exonerate:cdna2genome 2.4.0
+##date 2021-02-03
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+ENSG00000214643/1-4245 exonerate:cdna2genome gene 822 4162 885 + . gene_id 0 ; sequence CDS|ENST00000398721/1-183 ; gene_orientation + ; identity 99.45 ; similarity 99.45
+ENSG00000214643/1-4245 exonerate:cdna2genome utr5 822 880 . + .
+ENSG00000214643/1-4245 exonerate:cdna2genome exon 822 880 . + . insertions 0 ; deletions 0 ; identity 98.33 ; similarity 98.33
+ENSG00000214643/1-4245 exonerate:cdna2genome splice5 881 882 . + . intron_id 1 ; splice_site "GT"
+ENSG00000214643/1-4245 exonerate:cdna2genome intron 881 4038 . + . intron_id 1
+ENSG00000214643/1-4245 exonerate:cdna2genome splice3 4037 4038 . + . intron_id 0 ; splice_site "AC"
+ENSG00000214643/1-4245 exonerate:cdna2genome exon 4039 4162 . + . insertions 0 ; deletions 0 ; identity 99.19 ; similarity 99.19
+ENSG00000214643/1-4245 exonerate:cdna2genome similarity 822 4162 885 + . alignment_id 0 ; Query CDS|ENST00000398721/1-183 ; Align 822 1 59 ; Align 4039 60 124
+##FASTA
+>ENSG00000214643/1-4245 chromosome:GRCh38:6:49946021:49950265:-1
+CTCCTGCCTCAGCCTCTGGGAGTAGCTGGGACTACAGGGGCCCGCCACCACGCCCGGATAATTTTTTTCTAT
+TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCGGGACGGTCTTAATCTCCTGACCTAGTTATCCGCCAGC
+CTCGGCCTCCCAAAGTGCTGGAATTACGGGTGTGAGTATATTGCTTTTTAAATTCACTAGTTTATTCATTAT
+GTATAGCTATTTAAAAAAGAGAAAAACTGTCCTGGCTAACACGGTGAAACCCCGTTTCTACTAAAAATACAA
+AAAATTAGCCGGCCTGGTGGCGGGTGCCTGTAGTACCACCTACTCTGGAGGCTGAGGCAGGAGAATGGCGTG
+AACCCGGGAGGCAGAGCTTGCAGTGAGTCGCGATCGCGCCACTGAACTCCAGCCTGGGTGACAGAACGAGAC
+TCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGAAACTAAATCAAAAG
+CAAAGATTAAATTCTCATGCTTCTACTTTTCAGACCTTCAATAGGAGATTCTCAGTGGCATGCACTTCCTAG
+ACAACCAGTTATTAAAAAGATAATTATATACTATGGATATCATAACCCTTTATATCCCAAGATAAAAGAAAA
+GTAATGTCCTGCATTTTTGCCCCAGGCACTGCTAAACAGGAGTGTTAACTTTTGATAAACCCCAGTTTCTAA
+ATTCGTACAACTGCATGGAGAGAAGTATAAAAAGATGTGCTCTCCACCTTTCTCTTATTCAAACACTGCAGA
+GCTGCTAATTCGGCTGACTGTCTTCAATCATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGG
+TCCCCATTGCCACCAGGTAAAATGTAAATATTGAGAGGGTAAAATATCTTTCTGGAGAGTTGCATTTTGGTC
+GATGTCAACTGGAGACACAAGAGTGACCAGATTGTTAAGAGAGTGGTTGGTTACGGTCCCAAGAGTAAATCA
+CAAATAAAGGACTGTGGTCTTACTAAACAGTAAGGCTCCGGGTGAGTCATATTATTGTATGAGACAATTTAA
+AGGCCTTGATTAAATGACTACAGGCTGGTTGTCCAGACTGACTACTTGGATAGAATATTAAAGTATAACCAT
+CTGGATCCTTGAGACATTGATGGGCACTGTGTAGTAGAGTAACAGTTGGTTTTTCAGTAACCTCATGATAGG
+TTTGGTTATATTATGTCACAAGGTTTACTTTGAGAAAAACACAAAATGGTGTTTTCAACTGATTAAGAATTG
+AGAACTTCAGTGGCTGTATTACCTCAGGTCCAATTACATAGCAATTAATACTAACCAGATAATTAAATGAGT
+ATAAACTTTGGAATAATTGATACCTGGGTTCAGATTTGGCTTTTGCCATGTATTGGCTATGCAAATCTATCA
+GGTTATTTACACTCATTCAGCATCAATTTCCTCATTTGCGAATTAAATACAGTAATTAAGTCTATCTGTAGT
+ATTATGACGATTAATGATATTTAAATATACAAAATGCCCAACATAAAGTATAATACACATCAGATTCATCTT
+AAATAGTATTATAATTACTTTTACATTGTATTAAAACACCTTAAAAAGCAAGTAACATCTAGAAATCTCATC
+GAGAAACTCTTTCTTGACAACTATTGCAGGAAACAGGGGAGGTAATATTTACCATGTTGGATTTCACATACT
+TAAACTGTGTACCCTCATTTGTAAACTTTCATTGTACACACTACTATTAGATTAGATCAATAGCCAAAGGAA
+GTATCTTGATGGAGATCATCGAAAGAGCTGTTTTAACACATTTCAGGGTACTTATGATAGGAAAAGTATTTT
+TCTTATTTATGTAAAGACCCTGTAAACAATCATTTTACACACACCCAAGAAAATAATTCCACTCACCTTAAG
+AAAATAAAACAAACAAAAAAATAATAACTATAGGGCATTCTGATTTAGGAGTGGTCTAGAACTGCAAGAGTT
+TCCTCTTTGAAGTCCAACTTCATTCCTTAGCAGCACAGATGAGACCAAGGAAGTCTAGCTCTAACAATAAGT
+CTGGCTGTGAGTAAACTCAAACATCTAAGTATTTTGGATAAAAGACTCAAATCATTTTAATTGTTTTATAAT
+TCAAGTAAAATATGTCAGATGATAATTTTGAGGATTGTTATTTTATTACATCATTCTAAACTCAAGACTAAT
+GGAATTACAATCAGGGTTTGTTTTTACTAAAACCATATGGGGGTGATCTTAAAATAAAGAAGACTTATTTAG
+TGCAACCACATTTGGATAATAAAATTAGCTCCAGTTATGTTATCATGATTTACATGTGTGCCTCATGTCACT
+TGCTTTGGGAAAAAAGGTGAAAATTTTCATGACATTTTCAGTTTCATTATAAACCCAAGAGACATTATGAAT
+GTATGTGCATAGATTCATCTAAAAATTGAGAAATTTGTGATTCCTTCTTGTACATAAATAAATTTTTATGTT
+ATACATAGCTGTTATCTAGAGAGAAGCTGTTTGTTGTTTTTGTTACTAGTGGAAAAATGCTAATTTACAATT
+CCCACTTAAATAATGCTATTCTTTTTTTAATACTAGTGTTTGACAGCTGTCATCTTCTATTATTTGTAAATT
+CCAATTAAGTCAACATACATGCTTCACACCCATCATGTAGGACAGTGTAATCTGAGGATGCATTTTTAAGCT
+GGCAAGATAATGCTTTTTCCCTCTGGCATCAAAGGCAATAAATAGCATCTCTCTAGATAATACAAATAAAGA
+GATATCTATCATTAATTTATACAGTGAAAAAGCATATCTCGTTGCCTAAAATATTTGGCAAAAAATTCAAAA
+TAATATGTTCAATTTTTTCCTAAAATGTCTAGTTACTCCAAGTAACAGTAAGACTGTATGCTAACATAACTT
+CACTGAAAGCAGATGACATGAATTGGGTTATCAGTACCTTTGACTCCATCTCAGTTGGATCCTATATGTTGA
+GCACCTAGAGAAAGAGCACCTTTCACATACCTTTGTCACTGATATTTGATAATTTACCATTACATTTAATGC
+TTTAACTTTGGGCGTCTTCCTCCTTATGTGACCTTTCTAAAAATTTAAACATTTTGTGAAGAGATGAAACAT
+TAAGTCTTATGGCCAGATGTAGATGAGTTCATCAGCTGGTATATGCTATGATGATGCAATCCTGAGAACTTT
+ATAAAGGAGAAGACTCTGAAACAAGGAAACATACGGAGATGCTGAGAGATACTACCTCTTTCTCTTTGAACT
+TAAGGCTTGTCATTCATGACAACACTCATCCCCCCAGCAAACCAGGCTCCTGCCTAGGCTCAAATCTTTGTG
+AATATTCAAAGAACCTCTCTTATCCCAGTATCTGCTAGGGTTTTTTTCACTCTTCTAATAAAAGAGATTTAT
+AAAAAATATTCGAGCAAGATAGCAATTGAAGCAACATTAATGAATCTTCCCATTTTAAATCCTGAAACCAAA
+AATGTTTAAATGTTTAATTTTTTTTTTGAAATTGGAGAAAAAAGCCTTTGGGAGGTGATGGGATCATAGATA
+TTTGTATATGCCCAAATTCATCATTTGTACACATTAAATATGTGCAGTTCTTTTTATAGCAACTATACCTCA
+ATAAAGTTGTTTTTTTAAAAAAATCATGTTAGGTGGGTAGTAGGTAAGTAGCCATAGAAATATGTGGTGTTC
+ATTCCAGAACTACTTGAAATCTAACAATTTTTATTTAGAAATTCTCAGGGAAAACTAAGCTTTAACAACTAG
+TGGATCAAGCCAGAAGTTGGAGAGGAAACTGAGAATGAAACAGAAAGTATCACAGAACAATCATCACCAGAA
+AAATACAAAACAAATGACTTCCCAAATCCCTACCCCAGAATGCAAGGGCTATACTTATTTTCACATTGACAA
+CTGATTTATCCCAAGGTGGGACCTTAAGACACTTATAGTGACTCAATGGTTTATGTGCTTTCTTTTTCCCCT
+TTTAACAGTGAAATGTGCCGTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTG
+TCATGATTTTGAAAAACCAATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATGTAGAAGTTTGAAAT
+AAAAATCAGCATCCCTCAAAAGTAAAGCACAGTGAGTACAAGGATTAGTAATAAAAGAAACTGAATTAC
+>CDS|ENST00000398721/1-183 DEFB133-201
+ATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGGTCCCCATTGCCACCAGGGTGAAATGTGCC
+GTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTGTCATGATTTTGAAAAACCA
+ATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATG
--- /dev/null
+##gff-version 2
+##source-version exonerate:coding2genome 2.4.0
+##date 2021-02-03
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+CDS|ENST00000398721/1-183 exonerate:coding2genome similarity 1 183 322 + . alignment_id 0 ; Target ENSG00000214643/1-4245 ; Align 1 822 57 ; Align 61 4040 123
+# --- END OF GFF DUMP ---
+#
+##FASTA
+>ENSG00000214643/1-4245 chromosome:GRCh38:6:49946021:49950265:-1
+CTCCTGCCTCAGCCTCTGGGAGTAGCTGGGACTACAGGGGCCCGCCACCACGCCCGGATAATTTTTTTCTAT
+TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCGGGACGGTCTTAATCTCCTGACCTAGTTATCCGCCAGC
+CTCGGCCTCCCAAAGTGCTGGAATTACGGGTGTGAGTATATTGCTTTTTAAATTCACTAGTTTATTCATTAT
+GTATAGCTATTTAAAAAAGAGAAAAACTGTCCTGGCTAACACGGTGAAACCCCGTTTCTACTAAAAATACAA
+AAAATTAGCCGGCCTGGTGGCGGGTGCCTGTAGTACCACCTACTCTGGAGGCTGAGGCAGGAGAATGGCGTG
+AACCCGGGAGGCAGAGCTTGCAGTGAGTCGCGATCGCGCCACTGAACTCCAGCCTGGGTGACAGAACGAGAC
+TCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGAAACTAAATCAAAAG
+CAAAGATTAAATTCTCATGCTTCTACTTTTCAGACCTTCAATAGGAGATTCTCAGTGGCATGCACTTCCTAG
+ACAACCAGTTATTAAAAAGATAATTATATACTATGGATATCATAACCCTTTATATCCCAAGATAAAAGAAAA
+GTAATGTCCTGCATTTTTGCCCCAGGCACTGCTAAACAGGAGTGTTAACTTTTGATAAACCCCAGTTTCTAA
+ATTCGTACAACTGCATGGAGAGAAGTATAAAAAGATGTGCTCTCCACCTTTCTCTTATTCAAACACTGCAGA
+GCTGCTAATTCGGCTGACTGTCTTCAATCATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGG
+TCCCCATTGCCACCAGGTAAAATGTAAATATTGAGAGGGTAAAATATCTTTCTGGAGAGTTGCATTTTGGTC
+GATGTCAACTGGAGACACAAGAGTGACCAGATTGTTAAGAGAGTGGTTGGTTACGGTCCCAAGAGTAAATCA
+CAAATAAAGGACTGTGGTCTTACTAAACAGTAAGGCTCCGGGTGAGTCATATTATTGTATGAGACAATTTAA
+AGGCCTTGATTAAATGACTACAGGCTGGTTGTCCAGACTGACTACTTGGATAGAATATTAAAGTATAACCAT
+CTGGATCCTTGAGACATTGATGGGCACTGTGTAGTAGAGTAACAGTTGGTTTTTCAGTAACCTCATGATAGG
+TTTGGTTATATTATGTCACAAGGTTTACTTTGAGAAAAACACAAAATGGTGTTTTCAACTGATTAAGAATTG
+AGAACTTCAGTGGCTGTATTACCTCAGGTCCAATTACATAGCAATTAATACTAACCAGATAATTAAATGAGT
+ATAAACTTTGGAATAATTGATACCTGGGTTCAGATTTGGCTTTTGCCATGTATTGGCTATGCAAATCTATCA
+GGTTATTTACACTCATTCAGCATCAATTTCCTCATTTGCGAATTAAATACAGTAATTAAGTCTATCTGTAGT
+ATTATGACGATTAATGATATTTAAATATACAAAATGCCCAACATAAAGTATAATACACATCAGATTCATCTT
+AAATAGTATTATAATTACTTTTACATTGTATTAAAACACCTTAAAAAGCAAGTAACATCTAGAAATCTCATC
+GAGAAACTCTTTCTTGACAACTATTGCAGGAAACAGGGGAGGTAATATTTACCATGTTGGATTTCACATACT
+TAAACTGTGTACCCTCATTTGTAAACTTTCATTGTACACACTACTATTAGATTAGATCAATAGCCAAAGGAA
+GTATCTTGATGGAGATCATCGAAAGAGCTGTTTTAACACATTTCAGGGTACTTATGATAGGAAAAGTATTTT
+TCTTATTTATGTAAAGACCCTGTAAACAATCATTTTACACACACCCAAGAAAATAATTCCACTCACCTTAAG
+AAAATAAAACAAACAAAAAAATAATAACTATAGGGCATTCTGATTTAGGAGTGGTCTAGAACTGCAAGAGTT
+TCCTCTTTGAAGTCCAACTTCATTCCTTAGCAGCACAGATGAGACCAAGGAAGTCTAGCTCTAACAATAAGT
+CTGGCTGTGAGTAAACTCAAACATCTAAGTATTTTGGATAAAAGACTCAAATCATTTTAATTGTTTTATAAT
+TCAAGTAAAATATGTCAGATGATAATTTTGAGGATTGTTATTTTATTACATCATTCTAAACTCAAGACTAAT
+GGAATTACAATCAGGGTTTGTTTTTACTAAAACCATATGGGGGTGATCTTAAAATAAAGAAGACTTATTTAG
+TGCAACCACATTTGGATAATAAAATTAGCTCCAGTTATGTTATCATGATTTACATGTGTGCCTCATGTCACT
+TGCTTTGGGAAAAAAGGTGAAAATTTTCATGACATTTTCAGTTTCATTATAAACCCAAGAGACATTATGAAT
+GTATGTGCATAGATTCATCTAAAAATTGAGAAATTTGTGATTCCTTCTTGTACATAAATAAATTTTTATGTT
+ATACATAGCTGTTATCTAGAGAGAAGCTGTTTGTTGTTTTTGTTACTAGTGGAAAAATGCTAATTTACAATT
+CCCACTTAAATAATGCTATTCTTTTTTTAATACTAGTGTTTGACAGCTGTCATCTTCTATTATTTGTAAATT
+CCAATTAAGTCAACATACATGCTTCACACCCATCATGTAGGACAGTGTAATCTGAGGATGCATTTTTAAGCT
+GGCAAGATAATGCTTTTTCCCTCTGGCATCAAAGGCAATAAATAGCATCTCTCTAGATAATACAAATAAAGA
+GATATCTATCATTAATTTATACAGTGAAAAAGCATATCTCGTTGCCTAAAATATTTGGCAAAAAATTCAAAA
+TAATATGTTCAATTTTTTCCTAAAATGTCTAGTTACTCCAAGTAACAGTAAGACTGTATGCTAACATAACTT
+CACTGAAAGCAGATGACATGAATTGGGTTATCAGTACCTTTGACTCCATCTCAGTTGGATCCTATATGTTGA
+GCACCTAGAGAAAGAGCACCTTTCACATACCTTTGTCACTGATATTTGATAATTTACCATTACATTTAATGC
+TTTAACTTTGGGCGTCTTCCTCCTTATGTGACCTTTCTAAAAATTTAAACATTTTGTGAAGAGATGAAACAT
+TAAGTCTTATGGCCAGATGTAGATGAGTTCATCAGCTGGTATATGCTATGATGATGCAATCCTGAGAACTTT
+ATAAAGGAGAAGACTCTGAAACAAGGAAACATACGGAGATGCTGAGAGATACTACCTCTTTCTCTTTGAACT
+TAAGGCTTGTCATTCATGACAACACTCATCCCCCCAGCAAACCAGGCTCCTGCCTAGGCTCAAATCTTTGTG
+AATATTCAAAGAACCTCTCTTATCCCAGTATCTGCTAGGGTTTTTTTCACTCTTCTAATAAAAGAGATTTAT
+AAAAAATATTCGAGCAAGATAGCAATTGAAGCAACATTAATGAATCTTCCCATTTTAAATCCTGAAACCAAA
+AATGTTTAAATGTTTAATTTTTTTTTTGAAATTGGAGAAAAAAGCCTTTGGGAGGTGATGGGATCATAGATA
+TTTGTATATGCCCAAATTCATCATTTGTACACATTAAATATGTGCAGTTCTTTTTATAGCAACTATACCTCA
+ATAAAGTTGTTTTTTTAAAAAAATCATGTTAGGTGGGTAGTAGGTAAGTAGCCATAGAAATATGTGGTGTTC
+ATTCCAGAACTACTTGAAATCTAACAATTTTTATTTAGAAATTCTCAGGGAAAACTAAGCTTTAACAACTAG
+TGGATCAAGCCAGAAGTTGGAGAGGAAACTGAGAATGAAACAGAAAGTATCACAGAACAATCATCACCAGAA
+AAATACAAAACAAATGACTTCCCAAATCCCTACCCCAGAATGCAAGGGCTATACTTATTTTCACATTGACAA
+CTGATTTATCCCAAGGTGGGACCTTAAGACACTTATAGTGACTCAATGGTTTATGTGCTTTCTTTTTCCCCT
+TTTAACAGTGAAATGTGCCGTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTG
+TCATGATTTTGAAAAACCAATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATGTAGAAGTTTGAAAT
+AAAAATCAGCATCCCTCAAAAGTAAAGCACAGTGAGTACAAGGATTAGTAATAAAAGAAACTGAATTAC
+>CDS|ENST00000398721/1-183 DEFB133-201
+ATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGGTCCCCATTGCCACCAGGGTGAAATGTGCC
+GTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTGTCATGATTTTGAAAAACCA
+ATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATG
--- /dev/null
+##gff-version 2
+##source-version exonerate:coding2genome 2.4.0
+##date 2021-02-03
+##type DNA
+#
+#
+# seqname source feature start end score strand frame attributes
+#
+ENSG00000214643/1-4245 exonerate:coding2genome gene 822 4162 322 + . gene_id 0 ; sequence CDS|ENST00000398721/1-183 ; gene_orientation + ; identity 100.00 ; similarity 100.00
+ENSG00000214643/1-4245 exonerate:coding2genome cds 822 880 . + .
+ENSG00000214643/1-4245 exonerate:coding2genome exon 822 880 . + . insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
+ENSG00000214643/1-4245 exonerate:coding2genome splice5 881 882 . + . intron_id 1 ; splice_site "GT"
+ENSG00000214643/1-4245 exonerate:coding2genome intron 881 4038 . + . intron_id 1
+ENSG00000214643/1-4245 exonerate:coding2genome splice3 4037 4038 . + . intron_id 0 ; splice_site "AC"
+ENSG00000214643/1-4245 exonerate:coding2genome cds 4039 4162 . + .
+ENSG00000214643/1-4245 exonerate:coding2genome exon 4039 4162 . + . insertions 0 ; deletions 0 ; identity 100.00 ; similarity 100.00
+ENSG00000214643/1-4245 exonerate:coding2genome similarity 822 4162 322 + . alignment_id 0 ; Query CDS|ENST00000398721/1-183 ; Align 822 1 57 ; Align 4040 61 123
+##FASTA
+>ENSG00000214643/1-4245 chromosome:GRCh38:6:49946021:49950265:-1
+CTCCTGCCTCAGCCTCTGGGAGTAGCTGGGACTACAGGGGCCCGCCACCACGCCCGGATAATTTTTTTCTAT
+TTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCGGGACGGTCTTAATCTCCTGACCTAGTTATCCGCCAGC
+CTCGGCCTCCCAAAGTGCTGGAATTACGGGTGTGAGTATATTGCTTTTTAAATTCACTAGTTTATTCATTAT
+GTATAGCTATTTAAAAAAGAGAAAAACTGTCCTGGCTAACACGGTGAAACCCCGTTTCTACTAAAAATACAA
+AAAATTAGCCGGCCTGGTGGCGGGTGCCTGTAGTACCACCTACTCTGGAGGCTGAGGCAGGAGAATGGCGTG
+AACCCGGGAGGCAGAGCTTGCAGTGAGTCGCGATCGCGCCACTGAACTCCAGCCTGGGTGACAGAACGAGAC
+TCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAGAGAGAGAGAGAGAGAGAGAGAGAAACTAAATCAAAAG
+CAAAGATTAAATTCTCATGCTTCTACTTTTCAGACCTTCAATAGGAGATTCTCAGTGGCATGCACTTCCTAG
+ACAACCAGTTATTAAAAAGATAATTATATACTATGGATATCATAACCCTTTATATCCCAAGATAAAAGAAAA
+GTAATGTCCTGCATTTTTGCCCCAGGCACTGCTAAACAGGAGTGTTAACTTTTGATAAACCCCAGTTTCTAA
+ATTCGTACAACTGCATGGAGAGAAGTATAAAAAGATGTGCTCTCCACCTTTCTCTTATTCAAACACTGCAGA
+GCTGCTAATTCGGCTGACTGTCTTCAATCATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGG
+TCCCCATTGCCACCAGGTAAAATGTAAATATTGAGAGGGTAAAATATCTTTCTGGAGAGTTGCATTTTGGTC
+GATGTCAACTGGAGACACAAGAGTGACCAGATTGTTAAGAGAGTGGTTGGTTACGGTCCCAAGAGTAAATCA
+CAAATAAAGGACTGTGGTCTTACTAAACAGTAAGGCTCCGGGTGAGTCATATTATTGTATGAGACAATTTAA
+AGGCCTTGATTAAATGACTACAGGCTGGTTGTCCAGACTGACTACTTGGATAGAATATTAAAGTATAACCAT
+CTGGATCCTTGAGACATTGATGGGCACTGTGTAGTAGAGTAACAGTTGGTTTTTCAGTAACCTCATGATAGG
+TTTGGTTATATTATGTCACAAGGTTTACTTTGAGAAAAACACAAAATGGTGTTTTCAACTGATTAAGAATTG
+AGAACTTCAGTGGCTGTATTACCTCAGGTCCAATTACATAGCAATTAATACTAACCAGATAATTAAATGAGT
+ATAAACTTTGGAATAATTGATACCTGGGTTCAGATTTGGCTTTTGCCATGTATTGGCTATGCAAATCTATCA
+GGTTATTTACACTCATTCAGCATCAATTTCCTCATTTGCGAATTAAATACAGTAATTAAGTCTATCTGTAGT
+ATTATGACGATTAATGATATTTAAATATACAAAATGCCCAACATAAAGTATAATACACATCAGATTCATCTT
+AAATAGTATTATAATTACTTTTACATTGTATTAAAACACCTTAAAAAGCAAGTAACATCTAGAAATCTCATC
+GAGAAACTCTTTCTTGACAACTATTGCAGGAAACAGGGGAGGTAATATTTACCATGTTGGATTTCACATACT
+TAAACTGTGTACCCTCATTTGTAAACTTTCATTGTACACACTACTATTAGATTAGATCAATAGCCAAAGGAA
+GTATCTTGATGGAGATCATCGAAAGAGCTGTTTTAACACATTTCAGGGTACTTATGATAGGAAAAGTATTTT
+TCTTATTTATGTAAAGACCCTGTAAACAATCATTTTACACACACCCAAGAAAATAATTCCACTCACCTTAAG
+AAAATAAAACAAACAAAAAAATAATAACTATAGGGCATTCTGATTTAGGAGTGGTCTAGAACTGCAAGAGTT
+TCCTCTTTGAAGTCCAACTTCATTCCTTAGCAGCACAGATGAGACCAAGGAAGTCTAGCTCTAACAATAAGT
+CTGGCTGTGAGTAAACTCAAACATCTAAGTATTTTGGATAAAAGACTCAAATCATTTTAATTGTTTTATAAT
+TCAAGTAAAATATGTCAGATGATAATTTTGAGGATTGTTATTTTATTACATCATTCTAAACTCAAGACTAAT
+GGAATTACAATCAGGGTTTGTTTTTACTAAAACCATATGGGGGTGATCTTAAAATAAAGAAGACTTATTTAG
+TGCAACCACATTTGGATAATAAAATTAGCTCCAGTTATGTTATCATGATTTACATGTGTGCCTCATGTCACT
+TGCTTTGGGAAAAAAGGTGAAAATTTTCATGACATTTTCAGTTTCATTATAAACCCAAGAGACATTATGAAT
+GTATGTGCATAGATTCATCTAAAAATTGAGAAATTTGTGATTCCTTCTTGTACATAAATAAATTTTTATGTT
+ATACATAGCTGTTATCTAGAGAGAAGCTGTTTGTTGTTTTTGTTACTAGTGGAAAAATGCTAATTTACAATT
+CCCACTTAAATAATGCTATTCTTTTTTTAATACTAGTGTTTGACAGCTGTCATCTTCTATTATTTGTAAATT
+CCAATTAAGTCAACATACATGCTTCACACCCATCATGTAGGACAGTGTAATCTGAGGATGCATTTTTAAGCT
+GGCAAGATAATGCTTTTTCCCTCTGGCATCAAAGGCAATAAATAGCATCTCTCTAGATAATACAAATAAAGA
+GATATCTATCATTAATTTATACAGTGAAAAAGCATATCTCGTTGCCTAAAATATTTGGCAAAAAATTCAAAA
+TAATATGTTCAATTTTTTCCTAAAATGTCTAGTTACTCCAAGTAACAGTAAGACTGTATGCTAACATAACTT
+CACTGAAAGCAGATGACATGAATTGGGTTATCAGTACCTTTGACTCCATCTCAGTTGGATCCTATATGTTGA
+GCACCTAGAGAAAGAGCACCTTTCACATACCTTTGTCACTGATATTTGATAATTTACCATTACATTTAATGC
+TTTAACTTTGGGCGTCTTCCTCCTTATGTGACCTTTCTAAAAATTTAAACATTTTGTGAAGAGATGAAACAT
+TAAGTCTTATGGCCAGATGTAGATGAGTTCATCAGCTGGTATATGCTATGATGATGCAATCCTGAGAACTTT
+ATAAAGGAGAAGACTCTGAAACAAGGAAACATACGGAGATGCTGAGAGATACTACCTCTTTCTCTTTGAACT
+TAAGGCTTGTCATTCATGACAACACTCATCCCCCCAGCAAACCAGGCTCCTGCCTAGGCTCAAATCTTTGTG
+AATATTCAAAGAACCTCTCTTATCCCAGTATCTGCTAGGGTTTTTTTCACTCTTCTAATAAAAGAGATTTAT
+AAAAAATATTCGAGCAAGATAGCAATTGAAGCAACATTAATGAATCTTCCCATTTTAAATCCTGAAACCAAA
+AATGTTTAAATGTTTAATTTTTTTTTTGAAATTGGAGAAAAAAGCCTTTGGGAGGTGATGGGATCATAGATA
+TTTGTATATGCCCAAATTCATCATTTGTACACATTAAATATGTGCAGTTCTTTTTATAGCAACTATACCTCA
+ATAAAGTTGTTTTTTTAAAAAAATCATGTTAGGTGGGTAGTAGGTAAGTAGCCATAGAAATATGTGGTGTTC
+ATTCCAGAACTACTTGAAATCTAACAATTTTTATTTAGAAATTCTCAGGGAAAACTAAGCTTTAACAACTAG
+TGGATCAAGCCAGAAGTTGGAGAGGAAACTGAGAATGAAACAGAAAGTATCACAGAACAATCATCACCAGAA
+AAATACAAAACAAATGACTTCCCAAATCCCTACCCCAGAATGCAAGGGCTATACTTATTTTCACATTGACAA
+CTGATTTATCCCAAGGTGGGACCTTAAGACACTTATAGTGACTCAATGGTTTATGTGCTTTCTTTTTCCCCT
+TTTAACAGTGAAATGTGCCGTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTG
+TCATGATTTTGAAAAACCAATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATGTAGAAGTTTGAAAT
+AAAAATCAGCATCCCTCAAAAGTAAAGCACAGTGAGTACAAGGATTAGTAATAAAAGAAACTGAATTAC
+>CDS|ENST00000398721/1-183 DEFB133-201
+ATGAAGATTCACGTCTTTCTCTTTGTTTTATTTTTCTTTCTGGTCCCCATTGCCACCAGGGTGAAATGTGCC
+GTGAAAGACACCTATAGTTGCTTTATCATGAGAGGCAAATGTCGACATGAGTGTCATGATTTTGAAAAACCA
+ATTGGTTTCTGCACAAAACTAAATGCCAACTGTTATATG
import jalview.util.MapList;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.List;
import java.util.Map;
}
/*
- * locate the mapped sequence in the alignment or 'new' (GFF file) sequences;
+ * similarity start and end can tell us
+ * which part of the alignment refers to which sequence
*/
- SequenceI mappedSequence = findSequence(mapTo.get(0), align, newseqs,
- relaxedIdMatching);
-
- /*
- * If mapping is from protein to dna, we store it as dna to protein instead
- */
- SequenceI mapFromSequence = seq;
- SequenceI mapToSequence = mappedSequence;
- if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
- || (type == MappingType.PeptideToNucleotide
- && !featureIsOnTarget))
- {
- mapFromSequence = mappedSequence;
- mapToSequence = seq;
+ int similarityFrom,similarityTo;
+ try {
+ similarityFrom = Integer.parseInt(gff[START_COL]);
+ similarityTo = Integer.parseInt(gff[END_COL]);
+ } catch (Exception x) {
+ throw new IOException("Couldn't parse start/end of the similarity feature",x);
}
/*
*/
/*
- * get any existing mapping for these sequences (or start one),
- * and add this mapped range
- */
- AlignedCodonFrame acf = getMapping(align, mapFromSequence,
- mapToSequence);
-
- /*
* exonerate GFF has the strand of the target in column 7
* (differs from GFF3 which has it in the Target descriptor)
*/
}
List<String> alignedRegions = set.get(ALIGN);
+ List<MapList> mappings = new ArrayList<MapList>();
+ int fromLowest=0, fromHighest=0, toLowest=0, toHighest=0;
for (String region : alignedRegions)
{
MapList mapping = buildMapping(region, type, forwardStrand,
continue;
}
+ /*
+ * record total extent of aligned region(s) for later
+ */
+ if (mappings.size() == 0)
+ {
+ if (mapping.getFromLowest() < mapping.getFromHighest())
+ {
+ fromLowest = mapping.getFromLowest();
+ fromHighest = mapping.getFromHighest();
+ }
+ else
+ {
+ fromLowest = mapping.getFromHighest();
+ fromHighest = mapping.getFromLowest();
+ }
+ if (mapping.getToLowest() < mapping.getToHighest())
+ {
+ toLowest = mapping.getToLowest();
+ toHighest = mapping.getToHighest();
+ }
+ else
+ {
+ toLowest = mapping.getToHighest();
+ toHighest = mapping.getToLowest();
+ }
+ }
+ else
+ {
+ int fl = mapping.getFromLowest(), fh = mapping.getFromHighest(),
+ tl = mapping.getToLowest(), th = mapping.getToHighest();
+ if (fl > fh)
+ {
+ fl = fh;
+ fh = mapping.getFromLowest();
+ }
+ if (tl > th)
+ {
+ tl = th;
+ th = mapping.getToLowest();
+ }
+ if (fromLowest > fl)
+
+ {
+ fromLowest = fl;
+ }
+ if (fromHighest < fh)
+ {
+ fromHighest = fh;
+ }
+ if (toLowest > tl)
+ {
+ toLowest = tl;
+ }
+ if (toHighest < th)
+ {
+ toHighest = th;
+ }
+ }
+ mappings.add(mapping);
+ }
+
+ /*
+ * locate the mapped sequence in the alignment or 'new' (GFF file) sequences;
+ */
+ SequenceI mappedSequence = findSequence(mapTo.get(0), align, newseqs,
+ relaxedIdMatching);
+
+ /*
+ * finally, resolve the sense of the mapping
+ */
+ SequenceI mapFromSequence = seq;
+ SequenceI mapToSequence = mappedSequence;
+
+ /*
+ * If mapping is from protein to dna, we store it as dna to protein instead
+ */
+ if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
+ || (type == MappingType.PeptideToNucleotide
+ && !featureIsOnTarget))
+ {
+ mapFromSequence = mappedSequence;
+ mapToSequence = seq;
+ }
+ /*
+ * the sense of 'align' mappings for nucleotide alignments
+ * from exonerate seem to be ambiguous, so we need to do a bit more work
+ */
+ if (type == MappingType.NucleotideToNucleotide || type == MappingType.PeptideToPeptide)
+ {
+ /*
+ * then check whether the aligned region is contained
+ * by the feature to determine sense of mapping
+ */
+ if (fromHighest==toHighest && fromLowest==toLowest)
+ {
+ // ambiguous case - for simple alignments this doesn't matter, but important for rearrangements or inversions
+ if (featureIsOnTarget)
+ {
+ // TODO: raise a warning since we don't have test coverage for this case
+ mapFromSequence=mappedSequence; // Target sequence
+ mapToSequence=seq; // annotated sequence
+ }
+ } else if (similarityFrom == fromLowest && similarityTo == fromHighest)
+ {
+ mapFromSequence = seq;
+ mapToSequence = mappedSequence;
+ }
+ else if (similarityFrom == toLowest && similarityTo == toHighest)
+ {
+ mapFromSequence = mappedSequence;
+ mapToSequence = seq;
+ }
+ else
+ {
+ throw new IOException(
+ "Couldn't determine sense for similarity feature");
+ }
+ }
+
+ /*
+ * get any existing mapping for these sequences (or start one),
+ * and add this mapped range
+ */
+ AlignedCodonFrame acf = getMapping(align, mapFromSequence,
+ mapToSequence);
+ for (MapList mapping : mappings)
+ {
acf.addMap(mapFromSequence, mapToSequence, mapping);
}
align.addCodonFrame(acf);
assertEquals(2f, sf.getScore(), 0.001f);
}
+ @Test(groups = { "Functional" })
+ public void testImportGFF2ExonerateCDSAndCoding2Genome()
+ throws IOException
+ {
+ /*
+ * test assumes sequence 1 in imported alignment is a
+ * transcript shorter and aligned to exons on locus (sequence 0)
+ *
+ * exonerate script was - where mode was query or target
+ * exonerate --showvulgar false --showalignment false --show${mode}gff ... > test_${mode}.gff2
+ * echo '##FASTA' >> test_${mode}.gff2
+ * cat example_Locus.fa example_CDS.fa >> test_${mode}.gff2
+ * [ then edit out stuff before gff-version-2 header and the end of exonerate lines after the gff dump ]
+ */
+ String[][] testFiles = new String[][] {
+ { "test_cdna2genome_showquerygff.gff2",
+ "test_cdna2genome_showtargetgff.gff2" },
+ { "test_coding2genome_showquerygff.gff2",
+ "test_coding2genome_showtargetgff.gff2" } };
+
+ for (String[] testfilepair : testFiles)
+ {
+ FormatAdapter fa = new FormatAdapter();
+ AlignmentI al = fa.readFile("examples/testdata/" + testfilepair[0],
+ DataSourceType.FILE, FileFormat.Features);
+
+ assertEquals(2, al.getHeight());
+ // check there are gaps in sequence 1
+ assertTrue(al.getSequenceAt(1).getSequenceAsString().contains(""+al.getGapCharacter()));
+ assertTrue(al.isAligned());
+
+ AlignmentI al2 = fa.readFile("examples/testdata/" + testfilepair[1],
+ DataSourceType.FILE, FileFormat.Features);
+
+ assertEquals(2, al2.getHeight());
+ assertTrue(al2.isAligned());
+ // check sequence 1 is identical for alignment imported from both query and target gff
+ assertEquals(al.getSequenceAt(1).getSequenceAsString(),
+ al2.getSequenceAt(1).getSequenceAsString());
+ }
+ }
+
public static AlignmentI readAlignmentFile(File f) throws IOException
{
System.out.println("Reading file: " + f);
git://source.jalview.org / jalview.git / commitdiff