From b046afc929b241434a87cc57779cc111181f1fcb Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 10 Dec 2010 13:25:27 +0000 Subject: [PATCH] genbank.rb fixes git-svn-id: http://biopieces.googlecode.com/svn/trunk@1183 74ccb610-7750-0410-82ae-013aeee3265d --- bp_test/out/read_genbank.out.1 | 6 +++ bp_test/out/read_genbank.out.2 | 6 +++ bp_test/out/read_genbank.out.3 | 3 ++ bp_test/out/read_genbank.out.4 | 3 ++ code_ruby/Maasha/lib/genbank.rb | 76 ++++++++++++++++----------------- 5 files changed, 54 insertions(+), 40 deletions(-) diff --git a/bp_test/out/read_genbank.out.1 b/bp_test/out/read_genbank.out.1 index c27cb26..62c637a 100644 --- a/bp_test/out/read_genbank.out.1 +++ b/bp_test/out/read_genbank.out.1 @@ -16,6 +16,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgat +SEQ_LEN: 5027 STRAND: + S_BEG: 0 S_END: 5027 @@ -39,6 +40,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta +SEQ_LEN: 205 STRAND: + S_BEG: 0 S_END: 205 @@ -59,6 +61,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -85,6 +88,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -105,6 +109,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 @@ -129,6 +134,7 @@ TITLE: Cloning and sequence of REV7, a gene whose function is required forDNA da JOURNAL: Yeast 10 (11), 1503-1509 (1994);Genes Dev. 10 (7), 777-793 (1996);Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, NewHaven, CT, USA PUBMED: 7871890;8846915 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 diff --git a/bp_test/out/read_genbank.out.2 b/bp_test/out/read_genbank.out.2 index 0ae6772..5f85e9f 100644 --- a/bp_test/out/read_genbank.out.2 +++ b/bp_test/out/read_genbank.out.2 @@ -6,6 +6,7 @@ FEATURE: source LOCATOR: 1..5028 ACCESSION: U49845 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgtaacatatttaggatatacctcgaaaataataaaccgccacactgtcattattataattagaaacagaacgcaaaaattatccactatataattcaaagacgcgaaaaaaaaagaacaacgcgtcatagaacttttggcaattcgcgtcacaaataaattttggcaacttatgtttcctcttcgagcagtactcgagccctgtctcaagaatgtaataatacccatcgtaggtatggttaaagatagcatctccacaacctcaaagctccttgccgagagtcgccctcctttgtcgagtaattttcacttttcatatgagaacttattttcttattctttactctcacatcctgtagtgattgacactgcaacagccaccatcactagaagaacagaacaattacttaatagaaaaattatatcttcctcgaaacgatttcctgcttccaacatctacgtatatcaagaagcattcacttaccatgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtgattatacgcaacgatattttgcttaattttattttcctgttttattttttattagtggtttacagataccctatattttatttagtttttatacttagagacatttaattttaattccattcttcaaatttcatttttgcacttaaaacaaagatccaaaaatgctctcgccctcttcatattgagaatacactccattcaaaattttgtcgtcaccgctgattaatttttcactaaactgatgaataatcaaaggccccacgtcagaaccgactaaagaagtgagttttattttaggaggttgaaaaccattattgtctggtaaattttcatcttcttgacatttaacccagtttgaatccctttcaatttctgctttttcctccaaactatcgaccctcctgtttctgtccaacttatgtcctagttccaattcgatcgcattaataactgcttcaaatgttattgtgtcatcgttgactttaggtaatttctccaaatgcataatcaaactatttaaggaagatcggaattcgtcgaacacttcagtttccgtaatgatctgatcgtctttatccacatgttgtaattcactaaaatctaaaacgtatttttcaatgcataaatcgttctttttattaataatgcagatggaaaatctgtaaacgtgcgttaatttagaaagaacatccagtataagttcttctatatagtcaattaaagcaggatgcctattaatgggaacgaactgcggcaagttgaatgactggtaagtagtgtagtcgaatgactgaggtgggtatacatttctataaaataaaatcaaattaatgtagcattttaagtataccctcagccacttctctacccatctattcataaagctgacgcaacgattactattttttttttcttcttggatctcagtcgtcgcaaaaacgtataccttctttttccgaccttttttttagctttctggaaaagtttatattagttaaacagggtctagtcttagtgtgaaagctagtggtttcgattgactgatattaagaaagtggaaattaaattagtagtgtagacgtatatgcatatgtatttctcgcctgtttatgtttctacgtacttttgatttatagcaaggggaaaagaaatacatactattttttggtaaaggtgaaagcataatgtaaaagctagaataaaatggacgaaataaagagaggcttagttcatcttttttccaaaaagcacccaatgataataactaaaatgaaaaggatttgccatctgtcagcaacatcagttgtgtgagcaataataaaatcatcacctccgttgcctttagcgcgtttgtcgtttgtatcttccgtaattttagtcttatcaatgggaatcataaattttccaatgaattagcaatttcgtccaattctttttgagcttcttcatatttgctttggaattcttcgcacttcttttcccattcatctctttcttcttccaaagcaacgatccttctacccatttgctcagagttcaaatcggcctctttcagtttatccattgcttccttcagtttggcttcactgtcttctagctgttgttctagatcctggtttttcttggtgtagttctcattattagatctcaagttattggagtcttcagccaattgctttgtatcagacaattgactctctaacttctccacttcactgtcgagttgctcgtttttagcggacaaagatttaatctcgttttctttttcagtgttagattgctctaattctttgagctgttctctcagctcctcatatttttcttgccatgactcagattctaattttaagctattcaatttctctttgat +SEQ_LEN: 5027 STRAND: + S_BEG: 0 S_END: 5027 @@ -18,6 +19,7 @@ FEATURE: CDS LOCATOR: <1..206 ACCESSION: U49845 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta +SEQ_LEN: 205 STRAND: + S_BEG: 0 S_END: 205 @@ -27,6 +29,7 @@ FEATURE: gene LOCATOR: 687..3158 ACCESSION: U49845 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -42,6 +45,7 @@ FEATURE: CDS LOCATOR: 687..3158 ACCESSION: U49845 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -51,6 +55,7 @@ FEATURE: gene LOCATOR: complement(3300..4037) ACCESSION: U49845 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 @@ -64,6 +69,7 @@ FEATURE: CDS LOCATOR: complement(3300..4037) ACCESSION: U49845 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 diff --git a/bp_test/out/read_genbank.out.3 b/bp_test/out/read_genbank.out.3 index 6c3def0..894c9da 100644 --- a/bp_test/out/read_genbank.out.3 +++ b/bp_test/out/read_genbank.out.3 @@ -6,6 +6,7 @@ FEATURE: CDS LOCATOR: <1..206 ACCESSION: U49845 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta +SEQ_LEN: 205 STRAND: + S_BEG: 0 S_END: 205 @@ -21,6 +22,7 @@ FEATURE: CDS LOCATOR: 687..3158 ACCESSION: U49845 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -34,6 +36,7 @@ FEATURE: CDS LOCATOR: complement(3300..4037) ACCESSION: U49845 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 diff --git a/bp_test/out/read_genbank.out.4 b/bp_test/out/read_genbank.out.4 index 7608151..ff9f8c9 100644 --- a/bp_test/out/read_genbank.out.4 +++ b/bp_test/out/read_genbank.out.4 @@ -3,6 +3,7 @@ FEATURE: CDS LOCATOR: <1..206 ACCESSION: U49845 SEQ: gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaagaaccgccaatagacaacatatgta +SEQ_LEN: 205 STRAND: + S_BEG: 0 S_END: 205 @@ -12,6 +13,7 @@ FEATURE: CDS LOCATOR: 687..3158 ACCESSION: U49845 SEQ: atgacacagcttcagatttcattattgctgacagctactatatcactactccatctagtagtggccacgccctatgaggcatatcctatcggaaaacaataccccccagtggcaagagtcaatgaatcgtttacatttcaaatttccaatgatacctataaatcgtctgtagacaagacagctcaaataacatacaattgcttcgacttaccgagctggctttcgtttgactctagttctagaacgttctcaggtgaaccttcttctgacttactatctgatgcgaacaccacgttgtatttcaatgtaatactcgagggtacggactctgccgacagcacgtctttgaacaatacataccaatttgttgttacaaaccgtccatccatctcgctatcgtcagatttcaatctattggcgttgttaaaaaactatggttatactaacggcaaaaacgctctgaaactagatcctaatgaagtcttcaacgtgacttttgaccgttcaatgttcactaacgaagaatccattgtgtcgtattacggacgttctcagttgtataatgcgccgttacccaattggctgttcttcgattctggcgagttgaagtttactgggacggcaccggtgataaactcggcgattgctccagaaacaagctacagttttgtcatcatcgctacagacattgaaggattttctgccgttgaggtagaattcgaattagtcatcggggctcaccagttaactacctctattcaaaatagtttgataatcaacgttactgacacaggtaacgtttcatatgacttacctctaaactatgtttatctcgatgacgatcctatttcttctgataaattgggttctataaacttattggatgctccagactgggtggcattagataatgctaccatttccgggtctgtcccagatgaattactcggtaagaactccaatcctgccaatttttctgtgtccatttatgatacttatggtgatgtgatttatttcaacttcgaagttgtctccacaacggatttgtttgccattagttctcttcccaatattaacgctacaaggggtgaatggttctcctactattttttgccttctcagtttacagactacgtgaatacaaacgtttcattagagtttactaattcaagccaagaccatgactgggtgaaattccaatcatctaatttaacattagctggagaagtgcccaagaatttcgacaagctttcattaggtttgaaagcgaaccaaggttcacaatctcaagagctatattttaacatcattggcatggattcaaagataactcactcaaaccacagtgcgaatgcaacgtccacaagaagttctcaccactccacctcaacaagttcttacacatcttctacttacactgcaaaaatttcttctacctccgctgctgctacttcttctgctccagcagcgctgccagcagccaataaaacttcatctcacaataaaaaagcagtagcaattgcgtgcggtgttgctatcccattaggcgttatcctagtagctctcatttgcttcctaatattctggagacgcagaagggaaaatccagacgatgaaaacttaccgcatgctattagtggacctgatttgaataatcctgcaaataaaccaaatcaagaaaacgctacacctttgaacaacccctttgatgatgatgcttcctcgtacgatgatacttcaatagcaagaagattggctgctttgaacactttgaaattggataaccactctgccactgaatctgatatttccagcgtggatgaaaagagagattctctatcaggtatgaatacatacaatgatcagttccaatcccaaagtaaagaagaattattagcaaaacccccagtacagcctccagagagcccgttctttgacccacagaataggtcttcttctgtgtatatggatagtgaaccagcagtaaataaatcctggcgatatactggcaacctgtcaccagtctctgatattgtcagagacagttacggatcacaaaaaactgttgatacagaaaaacttttcgatttagaagcaccagagaaggaaaaacgtacgtcaagggatgtcactatgtcttcactggacccttggaacagcaatattagcccttctcccgtaagaaaatcagtaacaccatcaccatataacgtaacgaagcatcgtaaccgccacttacaaaatattcaagactctcaaagcggtaaaaacggaatcactcccacaacaatgtcaacttcatcttctgacgattttgttccggttaaagatggtgaaaatttttgctgggtccatagcatggaaccagacagaagaccaagtaagaaaaggttagtagatttttcaaataagagtaatgtcaatgttggtcaagttaaggacattcacggacgcatcccagaaatgctgtg +SEQ_LEN: 2471 STRAND: + S_BEG: 686 S_END: 3157 @@ -21,6 +23,7 @@ FEATURE: CDS LOCATOR: complement(3300..4037) ACCESSION: U49845 SEQ: tgaatagatgggtagagaagtggctgagggtatacttaaaatgctacattaatttgattttattttatagaaatgtatacccacctcagtcattcgactacactacttaccagtcattcaacttgccgcagttcgttcccattaataggcatcctgctttaattgactatatagaagaacttatactggatgttctttctaaattaacgcacgtttacagattttccatctgcattattaataaaaagaacgatttatgcattgaaaaatacgttttagattttagtgaattacaacatgtggataaagacgatcagatcattacggaaactgaagtgttcgacgaattccgatcttccttaaatagtttgattatgcatttggagaaattacctaaagtcaacgatgacacaataacatttgaagcagttattaatgcgatcgaattggaactaggacataagttggacagaaacaggagggtcgatagtttggaggaaaaagcagaaattgaaagggattcaaactgggttaaatgtcaagaagatgaaaatttaccagacaataatggttttcaacctcctaaaataaaactcacttctttagtcggttctgacgtggggcctttgattattcatcagtttagtgaaaaattaatcagcggtgacgacaaaattttgaatggagtgtattctcaatatgaagagggcgagagcatttttggatctttgttttaa +SEQ_LEN: 737 STRAND: - S_BEG: 3299 S_END: 4036 diff --git a/code_ruby/Maasha/lib/genbank.rb b/code_ruby/Maasha/lib/genbank.rb index 1cd91eb..f52505f 100644 --- a/code_ruby/Maasha/lib/genbank.rb +++ b/code_ruby/Maasha/lib/genbank.rb @@ -67,10 +67,11 @@ class Genbank keys.each_pair { |key,val| record[key] = val } loc = Locator.new(record[:LOCATOR], seq) - record[:SEQ] = loc.subseq.seq - record[:STRAND] = loc.strand - record[:S_BEG] = loc.s_beg - record[:S_END] = loc.s_end + record[:SEQ] = loc.subseq.seq + record[:SEQ_LEN] = loc.subseq.length + record[:STRAND] = loc.strand + record[:S_BEG] = loc.s_beg + record[:S_END] = loc.s_end yield record end @@ -110,17 +111,16 @@ class Genbank # Method to get the DNA sequence from a Genbank entry and return # this as a Seq object. def get_seq - seq = Seq.new(nil, "", "dna") - i = @entry.size + i = @entry.size + j = i - 1 - while @entry[i] and @entry[i] !~ /^[A-Z]/ - if @entry[i] =~ /^\s{0,8}\d+(.+)/ - seq.seq << $1.delete(" ") - end - - i -= 1 + while @entry[j] and @entry[j] !~ /^[A-Z]/ + j -= 1 end - seq + + seq = @entry[j + 1 .. i].join.delete(" 0123456789") + + Seq.new(nil, seq, "dna") if seq end # Method to get the base keys from Genbank entry and return these @@ -275,18 +275,14 @@ class Locator attr_accessor :locator, :seq, :subseq def initialize(locator, seq) - @loc_orig = locator - @locator = locator - @seq = seq - @subseq = Seq.new(nil, "", "dna") - end - - def subseq - parse_locator + @locator = locator + @seq = seq + @subseq = Seq.new(nil, "", "dna") + parse_locator(locator) end def strand - if @loc_orig.match("complement") + if @locator.match("complement") return "-" else return "+" @@ -294,13 +290,13 @@ class Locator end def s_beg - if @loc_orig =~ /(\d+)/ + if @locator =~ /(\d+)/ return $1.to_i - 1 end end def s_end - if @loc_orig.reverse =~ /(\d+)/ + if @locator.reverse =~ /(\d+)/ return $1.reverse.to_i - 1 end end @@ -315,38 +311,38 @@ class Locator # list of ranges are stripped from operators, and the subsequence are # fetched and handled according to the operators. # SNP locators are also dealt with (single positions). - def parse_locator(join = nil, comp = nil, order = nil) - intervals = @locator.split(",") + def parse_locator(locator, join = nil, comp = nil, order = nil) + intervals = locator.split(",") unless balance_params?(intervals.first) # locator includes a join/comp/order of several ranges - case @locator + case locator when /^join\((.*)\)$/ - @locator = $1 + locator = $1 join = true when /^complement\((.*)\)$/ - @locator = $1 + locator = $1 comp = true when /^order\((.*)\)$/ - @locator = $1 + locator = $1 order = true end - parse_locator(join, comp, order) + parse_locator(locator, join, comp, order) else intervals.each do |interval| case interval when /^join\((.*)\)$/ - @locator = $1 - join = true - parse_locator(join, comp, order) + locator = $1 + join = true + parse_locator(locator, join, comp, order) when /^complement\((.*)\)$/ - @locator = $1 - comp = true - parse_locator(join, comp, order) + locator = $1 + comp = true + parse_locator(locator, join, comp, order) when /^order\((.*)\)$/ - @locator = $1 - order = true - parse_locator(join, comp, order) + locator = $1 + order = true + parse_locator(locator, join, comp, order) when /^[<>]?(\d+)[^\d]+(\d+)$/ int_beg = $1.to_i - 1 int_end = $2.to_i - 1 -- 2.39.5