| Previous changeset 2:321cad0eb507 (2021-03-16) Next changeset 4:ba6c4aeb22ea (2021-05-21) |
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Commit message:
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b" |
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modified:
cherry_pick_fasta.py cherry_pick_fasta.xml test-data/output.fa |
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added:
test-data/alt_termlist.txt test-data/output_alt_termlist.fa test-data/output_alt_termlist_without.fa test-data/output_exact.fa test-data/output_exactly_not.fa |
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| diff -r 321cad0eb507 -r c282a8a47dd9 cherry_pick_fasta.py --- a/cherry_pick_fasta.py Tue Mar 16 23:25:57 2021 +0000 +++ b/cherry_pick_fasta.py Fri May 21 09:34:14 2021 +0000 |
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| @@ -1,51 +1,63 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -""" -Chery pick of fasta sequences satisfying a query string in their header/name -""" +# Chery pick of fasta sequences satisfying a query string in their header/name +import argparse -import argparse +from Bio import SeqIO def Parser(): the_parser = argparse.ArgumentParser( - description="Cherry pick fasta sequences") - the_parser.add_argument('--input', action="store", type=str, - help="input fasta file") - the_parser.add_argument('--searchfor', action="store", type=str, - help="with, without, or withlist, withoutlist") - the_parser.add_argument('--query-string', dest="query_string", - action="store", type=str, - help="headers containing the string will be \ + description='Cherry pick fasta sequences') + the_parser.add_argument('--input', action='store', type=str, + help='input fasta file') + the_parser.add_argument('--searchfor', action='store', type=str, + help='with, without, or withlist, withoutlist') + the_parser.add_argument('--mode', action='store', type=str, + default='includes', help='exact or includes') + the_parser.add_argument('--query-string', dest='query_string', + action='store', type=str, + help='headers containing the string will be \ extracted or excluded as well as the \ - corresponding sequence") - the_parser.add_argument('--query-file', dest="query_file", - action="store", type=str, - help="headers containing any of the strings provided in the \ - text file (1 string per line) will be \ - extracted or excluded as well as the \ - corresponding sequence") - - the_parser.add_argument( - '--output', action="store", type=str, help="output fasta file") + corresponding sequence') + the_parser.add_argument('--query-file', dest='query_file', + action='store', type=str, + help='headers containing any of the strings \ + provided in the text file (1 string per \ + line) will be extracted or excluded as well \ + as the corresponding sequence') + the_parser.add_argument('--output', action='store', type=str, + help='output fasta file') args = the_parser.parse_args() return args -def parse_fasta_with(query, FastaListe): +def parse_fasta_dict(query, fasta_dict, mode): if not isinstance(query, list): query = [query] accumulator = [] - for sequence in FastaListe: - for string in query: - if string in sequence: - accumulator.append(sequence) - continue - return accumulator + if mode == 'includes': + for seq_id in fasta_dict: + for string in query: + if string in seq_id: + accumulator.append(seq_id) + continue + elif mode == 'exact': + for seq_id in fasta_dict: + for string in query: + if string == seq_id: + accumulator.append(seq_id) + continue + res_dict = {k: fasta_dict[k] for k in fasta_dict if k in accumulator} + return res_dict -def complement_fasta(fullfasta, subfasta): - return sorted(list(set(fullfasta) - set(subfasta))) +def complement_fasta_dict(fasta_dict, subfasta_dict): + fasta_ids = list(fasta_dict.keys()) + subfasta_ids = list(subfasta_dict.keys()) + complement_ids = list(set(fasta_ids) - set(subfasta_ids)) + sub_dict = {k: fasta_dict[k] for k in fasta_dict if k in complement_ids} + return sub_dict def getquerylist(file): @@ -55,37 +67,37 @@ return querylist -def __main__(): - """ main function """ - args = Parser() - searchterm = args.query_string - CrudeFasta = open(args.input, "r").read() - Output = open(args.output, "w") - FastaListe = CrudeFasta.split(">")[1:] - if args.query_string: - if args.searchfor == 'with': - contList = parse_fasta_with(searchterm, FastaListe) - contFasta = ">%s" % ">".join(contList) - Output.write(contFasta) - elif args.searchfor == 'without': - notcontList = complement_fasta(FastaListe, - parse_fasta_with(searchterm, - FastaListe)) - notcontFasta = ">%s" % ">".join(notcontList) - Output.write(notcontFasta) - if args.query_file: - searchlist = getquerylist(args.query_file) - if args.searchfor == 'with': - contList = parse_fasta_with(searchlist, FastaListe) - contFasta = ">%s" % ">".join(contList) - Output.write(contFasta) - elif args.searchfor == 'without': - notcontList = complement_fasta(FastaListe, parse_fasta_with( - searchlist, FastaListe)) - notcontFasta = ">%s" % ">".join(notcontList) - Output.write(notcontFasta) - Output.close() +def buid_fasta_dict(fasta): + seq_dict = {rec.id: rec.seq for rec in SeqIO.parse(fasta, "fasta")} + return seq_dict + + +def write_fasta_result(fasta_dict, file): + line_length = 60 + with open(file, 'w') as f: + for header in sorted(fasta_dict): + f.write('>%s\n' % header) + for i in range(line_length, len(fasta_dict[header]), line_length): + f.write('%s\n' % fasta_dict[header][i-line_length:i]) + f.write('%s\n' % fasta_dict[header][i:]) -if __name__ == "__main__": +def __main__(): + ''' main function ''' + args = Parser() + fasta_dict = buid_fasta_dict(args.input) + if args.query_string: + query = args.query_string + elif args.query_file: + query = getquerylist(args.query_file) + if args.searchfor == 'with': + fasta_result_dict = parse_fasta_dict(query, fasta_dict, args.mode) + elif args.searchfor == 'without': + fasta_result_dict = complement_fasta_dict(fasta_dict, parse_fasta_dict( + query, fasta_dict, + args.mode)) + write_fasta_result(fasta_result_dict, args.output) + + +if __name__ == '__main__': __main__() |
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| diff -r 321cad0eb507 -r c282a8a47dd9 cherry_pick_fasta.xml --- a/cherry_pick_fasta.xml Tue Mar 16 23:25:57 2021 +0000 +++ b/cherry_pick_fasta.xml Fri May 21 09:34:14 2021 +0000 |
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| @@ -1,15 +1,23 @@ -<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="2.1.0"> +<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="3.0.0"> <description>with header satisfying a string query</description> <requirements> - <requirement type="package" version="3.7.6">python</requirement> + <requirement type="package" version="1.70">biopython</requirement> </requirements> <command interpreter="python">cherry_pick_fasta.py --input $input --searchfor '$search.searchfor' #if $search.options_selector == 'single': - --query-string '$search.query' + #if $search.match == 'exact': + --query-string '$search.query' --mode exact + #else: + --query-string '$search.query' --mode includes + #end if #else: - --query-file '$search.query' + #if $search.match == 'exact': + --query-file '$search.query' --mode exact + #else: + --query-file '$search.query' --mode includes + #end if #end if --output $output </command> @@ -18,11 +26,19 @@ <param name="input" type="data" format="fasta" label="Source file" help="Fasta file to parse" /> <conditional name="search"> - <param name="options_selector" type="select" display="radio" label="by single term or file of terms"> - <option value="single" selected="True">single term</option> - <option value="textdataset">terms in a text dataset</option> + <param name="options_selector" type="select" display="radio" label="for a"> + <option value="single" selected="True">single string</option> + <option value="textdataset">list of strings</option> </param> <when value="single"> + <param name="match" type="select" label="retrieve sequences whose headers..."> + <option value="include" selected="true">partially</option> + <option value="exact">exactly</option> + </param> + <param name="searchfor" type="select" label=" "> + <option value="with" selected="true">contain this string</option> + <option value="without">do not contain this string</option> + </param> <param name="query" type="text" size="30" value="" label="Search string" help="exemple: gi|40557596"> <sanitizer> <valid initial="string.printable"> @@ -35,17 +51,17 @@ </mapping> </sanitizer> </param> - <param name="searchfor" type="select" label="retrieve sequences whose headers contain or do not contain the search string"> - <option value="with" selected="true">contain</option> - <option value="without">do not contain</option> - </param> </when> <when value="textdataset"> - <param name="query" type="data" format="txt" label="term dataset" help="a list of term to search for, one term per line" /> - <param name="searchfor" type="select" label="retrieve sequences whose headers contain or do not contain the search list"> - <option value="with" selected="true">contain</option> - <option value="without">do not contain</option> + <param name="match" type="select" label="retrieve sequences whose headers..."> + <option value="includes" selected="true">partially</option> + <option value="exact">exactly</option> </param> + <param name="searchfor" type="select" label=" "> + <option value="with" selected="true">contain one of these list strings</option> + <option value="without">do not contain one of these list strings</option> + </param> + <param name="query" type="data" format="txt" label="list of strings dataset" help="a list of strings to search for, one string per line" /> </when> </conditional> </inputs> @@ -53,16 +69,50 @@ <data name="output" format="fasta" label="Fasta sequences ${search.searchfor.value} ${search.options_selector} term(s) in header" /> </outputs> <tests> + <!-- exact matches --> + <test> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" /> + <param name="searchfor" value="without" /> + <param name="match" value="exact" /> + <output name="output" ftype="fasta" file="output_exactly_not.fa" /> + </test> + <test> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="query" value="gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122" /> + <param name="searchfor" value="with" /> + <param name="match" value="exact" /> + <output name="output" ftype="fasta" file="output_exact.fa" /> + </test> + + <test> <param ftype="fasta" name="input" value="input.fa" /> - <!-- <param name="options_selector" value="textdataset" /> --> + <param name="options_selector" value="textdataset" /> + <param name="query" ftype="txt" value="alt_termlist.txt" /> + <param name="searchfor" value="without" /> + <param name="match" value="exact" /> + <output name="output" ftype="fasta" file="output_alt_termlist_without.fa" /> + </test> + <test> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="options_selector" value="textdataset" /> + <param name="query" ftype="txt" value="alt_termlist.txt" /> + <param name="searchfor" value="with" /> + <param name="match" value="exact" /> + <output name="output" ftype="fasta" file="output_alt_termlist.fa" /> + </test> + + + <!-- partial matches --> + <test> + <param ftype="fasta" name="input" value="input.fa" /> <param name="query" value="gi|81971654" /> <param name="searchfor" value="with" /> <output name="output" ftype="fasta" file="output.fa" /> </test> <test> <param ftype="fasta" name="input" value="input.fa" /> - <!-- <param name="options_selector" value="textdataset" /> --> <param name="query" value="RNA" /> <param name="searchfor" value="without" /> <output name="output" ftype="fasta" file="output_without.fa" /> @@ -82,17 +132,11 @@ <output name="output" ftype="fasta" file="output_termlist_without.fa" /> </test> </tests> - <help> **What it does** This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match -or do not match a given string. - -It is Copyright © 2019 `CNRS and Sorbonne-Université`_ and is released under the `MIT license`_. - -.. _CNRS and Sorbonne-Université: http://www.sorbonne-universite.fr/en -.. _MIT license: http://opensource.org/licenses/MIT +or do not match a given string, or a list of strings. </help> </tool> |
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| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/alt_termlist.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alt_termlist.txt Fri May 21 09:34:14 2021 +0000 |
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| @@ -0,0 +1,5 @@ +Locus_65_ +Locus_63_ +Pro--Locus_50 +gi|21321709|ref|NP_647481.1|_nonstructural_polyprotein__Cricket_paralysis_virus--Locus_63_Transcript_2/2_Confidence_0.333_Length_343_hit1_IdMatch=50.86,AligLength=116,E-val=6e-30 +gi|2388673|gb|AAC58807.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=46.44,AligLength=450,E-val=8e-138 |
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| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/output.fa --- a/test-data/output.fa Tue Mar 16 23:25:57 2021 +0000 +++ b/test-data/output.fa Fri May 21 09:34:14 2021 +0000 |
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| @@ -1,27 +1,29 @@ ->gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122 -TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC -TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA -TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG -CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG -CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG -TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT -GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT -TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC -TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG -CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT -TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT -ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG -TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA -AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG -GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG -GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG -GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG -TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC -TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA -CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC -GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG -GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC -TCGATGTGTACGAATTCGTGCGC +>gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_50_Transcript_1/1_Confidence_0.000_Length_1442_hit1_IdMatch=24.95,AligLength=537,E-val=8e-47 +GAATTCGTGCGCATGCAAAGAATAAATGACCACCCTTCGGGTTGGAAAGCTACGGATGAA +GTATATGGCTATGCAGAGTTCTCGAAACTAATGTGTGCTGAATGGAAGAGAAGGAAGACA +GAACATCAGAATACTGTTGACTTCCTTAAGAAGTATGCAGAGCGACCCTTCGAGACCAAC +CCCGGACCAGTGGAGGATATCCCAATAAGACACGATGATGTCGAGCAGGGGGTAGAAGCG +CAGATGGGTCGAGATGCAGATTGGTTTAACAATGACATAGCGGAACGTATAGCGCGTGGA +CAGGATATTACTGATATCTTGTATGAGTATGCTGAAGATGACGAGTTGCATGAGGATTAC +ATGGCTTACAAGAAACAGCAGGCCCAGCCTAGTAAGTGGGACAAATACGCGCGCCGTCTC +GAAAGTGCAATTACGGAAGGAAAGAATTTCCTTGCCCGTGTGGTTTCAAAAATAGCCAGC +GTCATTCGGGAGAACCCATATTTGACCATGATGGCAACTGTGGGGAGCGTTCTCGCTCTG +TATGGAGCTATGCGTTGGTTTTCGAAAGGAGTAACGGAGACTTTTGACGCTGAAGAAGTT +ACTATTCCCAACGAAACCAAGGTAGAGAACGTTGTGCGTACGGAGGGTTTTGAATCTTAC +GACCATCGGACTCCGCGCGCTCATCGAGCCAACAGGCAATATGTGCGAGCTGAGGCGATG +ATAGATGAAACAGGGTACCTGGTAGCCAACAACAAAGTCACTGGCAACACGTATCGAATG +TGTATCAAGAGGGATCCTGATGATTTGGTCGTTGGAAACGCTGTGTTTATCACAGGGTGG +ACGCTCCTCATACCGTACCACTTCGTTTGTGGACTGGCGGGACGGAGAATAGCTGCTGAT +TCCATCGTGACTTTGTCAAAGCCAGGCTTGGATAAGATTATTGAATTCCCGTTGTCACGA +ATCTTCCGATACGATACCTCACCAGATGGTTTTACCACTAGTGAGTATTGTGCTCGAATG +GAACATGAAGATGGAGAATTGGTTGATGCCATCCTGGTAAACCTGCATGGTTTGGGAGTG +CGAATCCATCCTGACCTCCGGGGAAAAATTGTGACGGTACGAGACCAAGCGCACCTGAGT +ACGACATTTCATGCGATTCTCACAACGATGTCCAGGAAGCCACCACTAACAACGTCACAA +CAAGTGGTAAAAGGGGTCAAGCCAATGGATAAAATCCTGCACATCAATTTACCAGTTGGG +GACAAAACAACGCAATACACCCAACGTGACTGTTACAAGTATTATTCCGTAACGGTCGTT +GGAGATTGTGGTGCCTTGCTGGTAGCACAAAATCATGCAATTGTGAGGAAAATATTTGCA +ATGCATATAGCAGGTGCGGAAGAAAATGGCTATGCTTGTCCAATCAATCAGGAAATGTTA +G >gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_63_Transcript_1/2_Confidence_0.333_Length_1607_hit1_IdMatch=52.99,AligLength=536,E-val=0.0 CTAGAATCACAGCTCAGATGAGTTTTGAGGCACCGAAGGACGCAATTGAAGGACCGTGTC AAACCCCGGAAGGATTGTTCGCCCCTATTGGCAAAGCGCCGATAGGCGTAGGGATGTCCA @@ -50,32 +52,6 @@ ACCCAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACG GAAGGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTG AATATCCTCAA ->gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_50_Transcript_1/1_Confidence_0.000_Length_1442_hit1_IdMatch=24.95,AligLength=537,E-val=8e-47 -GAATTCGTGCGCATGCAAAGAATAAATGACCACCCTTCGGGTTGGAAAGCTACGGATGAA -GTATATGGCTATGCAGAGTTCTCGAAACTAATGTGTGCTGAATGGAAGAGAAGGAAGACA -GAACATCAGAATACTGTTGACTTCCTTAAGAAGTATGCAGAGCGACCCTTCGAGACCAAC -CCCGGACCAGTGGAGGATATCCCAATAAGACACGATGATGTCGAGCAGGGGGTAGAAGCG -CAGATGGGTCGAGATGCAGATTGGTTTAACAATGACATAGCGGAACGTATAGCGCGTGGA -CAGGATATTACTGATATCTTGTATGAGTATGCTGAAGATGACGAGTTGCATGAGGATTAC -ATGGCTTACAAGAAACAGCAGGCCCAGCCTAGTAAGTGGGACAAATACGCGCGCCGTCTC -GAAAGTGCAATTACGGAAGGAAAGAATTTCCTTGCCCGTGTGGTTTCAAAAATAGCCAGC -GTCATTCGGGAGAACCCATATTTGACCATGATGGCAACTGTGGGGAGCGTTCTCGCTCTG -TATGGAGCTATGCGTTGGTTTTCGAAAGGAGTAACGGAGACTTTTGACGCTGAAGAAGTT -ACTATTCCCAACGAAACCAAGGTAGAGAACGTTGTGCGTACGGAGGGTTTTGAATCTTAC -GACCATCGGACTCCGCGCGCTCATCGAGCCAACAGGCAATATGTGCGAGCTGAGGCGATG -ATAGATGAAACAGGGTACCTGGTAGCCAACAACAAAGTCACTGGCAACACGTATCGAATG -TGTATCAAGAGGGATCCTGATGATTTGGTCGTTGGAAACGCTGTGTTTATCACAGGGTGG -ACGCTCCTCATACCGTACCACTTCGTTTGTGGACTGGCGGGACGGAGAATAGCTGCTGAT -TCCATCGTGACTTTGTCAAAGCCAGGCTTGGATAAGATTATTGAATTCCCGTTGTCACGA -ATCTTCCGATACGATACCTCACCAGATGGTTTTACCACTAGTGAGTATTGTGCTCGAATG -GAACATGAAGATGGAGAATTGGTTGATGCCATCCTGGTAAACCTGCATGGTTTGGGAGTG -CGAATCCATCCTGACCTCCGGGGAAAAATTGTGACGGTACGAGACCAAGCGCACCTGAGT -ACGACATTTCATGCGATTCTCACAACGATGTCCAGGAAGCCACCACTAACAACGTCACAA -CAAGTGGTAAAAGGGGTCAAGCCAATGGATAAAATCCTGCACATCAATTTACCAGTTGGG -GACAAAACAACGCAATACACCCAACGTGACTGTTACAAGTATTATTCCGTAACGGTCGTT -GGAGATTGTGGTGCCTTGCTGGTAGCACAAAATCATGCAATTGTGAGGAAAATATTTGCA -ATGCATATAGCAGGTGCGGAAGAAAATGGCTATGCTTGTCCAATCAATCAGGAAATGTTA -G >gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_63_Transcript_2/2_Confidence_0.333_Length_343_hit1_IdMatch=50.86,AligLength=116,E-val=6e-30 ACACAGTCCACAGTCCGAAGACCAAAGCGTTGGATAGGACACGAATACACAGATGAAACG AAAACAGGCGAGGCTGCGCCCTATCGGACATTGGAAGAAGTCCGTTTCCTTAAAAGAGGG @@ -83,6 +59,30 @@ GAAATGCTTAATTGGACGCGCAAAGGGATTAACCCAGATGATGTGACGATGATGATCATT GATACAGCATTTAGGGAGATCTCTTATCACGGAAGGGAAGCTTTCGAGAAGCTGCGAGGG CAGATACTTGAGCAGCGGGATGTGTTGGTTGAATATCCTCAA +>gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122 +TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC +TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA +TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG +CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG +CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG +TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT +GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT +TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC +TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG +CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT +TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT +ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG +TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA +AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG +GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG +GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG +GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG +TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC +TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA +CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC +GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG +GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC +TCGATGTGTACGAATTCGTGCGC >gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_2/2_Confidence_0.333_Length_1324_hit1_IdMatch=43.5,AligLength=446,E-val=1e-119 CTTGAGGATACTTTACCAGGTATGGTCGAGCACGTTACGCTCGTAGCACAAAATACATCC GCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAATGCTTTGCATTGTTTTGATT |
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| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/output_alt_termlist.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_alt_termlist.fa Fri May 21 09:34:14 2021 +0000 |
| b |
| @@ -0,0 +1,31 @@ +>gi|21321709|ref|NP_647481.1|_nonstructural_polyprotein__Cricket_paralysis_virus--Locus_63_Transcript_2/2_Confidence_0.333_Length_343_hit1_IdMatch=50.86,AligLength=116,E-val=6e-30 +ACACAGTCCACAGTCCGAAGACCAAAGCGTTGGATAGGACACGAATACACAGATGAAACG +AAAACAGGCGAGGCTGCGCCCTATCGGACATTGGAAGAAGTCCGTTTCCTTAAAAGAGGG +TTCAGAATGGATCACCTCTTGTGTCGGTGGGTAGCTCCTTTGAAGAAGGATGTCATCTAC +GAAATGCTTAATTGGACGCGCAAAGGGATTAACCCAGATGATGTGACGATGATGATCATT +GATACAGCATTTAGGGAGATCTCTTATCACGGAAGGGAAGCTTTCGAGAAGCTGCGAGGG +CAGATACTTGAGCAGCGGGATGTGTTGGTTGAATATCCTCAA +>gi|2388673|gb|AAC58807.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=46.44,AligLength=450,E-val=8e-138 +TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC +TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA +TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG +CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG +CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG +TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT +GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT +TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC +TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG +CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT +TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT +ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG +TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA +AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG +GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG +GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG +GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG +TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC +TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA +CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC +GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG +GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC +TCGATGTGTACGAATTCGTGCGC |
| b |
| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/output_alt_termlist_without.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_alt_termlist_without.fa Fri May 21 09:34:14 2021 +0000 |
| b |
| b'@@ -0,0 +1,5874 @@\n+>gi|123840414|sp|Q2Y0E9.1|RDRP_APRVF_RecName:_Full_RNA-directed_RNA_polymerase_VP2--Locus_27_Transcript_1/7_Confidence_0.444_Length_3872_hit1_IdMatch=25.16,AligLength=1220,E-val=1e-82\n+TTATAGTACCTCAGAGTATTTTGAAGCCACCACCTTTCAACGAGAAAGACTGGCCTTTGA\n+ATGAAGACGAGAGTATGTTCAGTGCCTCGCGCAAGTATAATTACATGATAAATACTAGTA\n+CGTTGAGCCTTTATGGTTCGAGGGAAAGTTTAGTCGGTAAAGCAATATACGGTTTATATA\n+CTGATGAGCAATCACAGTCACGCTTCAGGACAGTATGGCATCAAATAATGGCAAGTGTCT\n+ACGCACTAGACGATTATCTAGGTCATACTAACCATCCAGTTCGTGCAGTGTTGGCACAGT\n+TAAACTTAGACAAAGGATTACCATTCAAGGAAACTGCTGAAGGTATTGACTTAACAGAGG\n+CGGTTGAAAAAGGAATTGATTCGAGTACATTACTACCATCAATATTATATATGTTGATCT\n+CAGTATCGTGCGATATCTGTTTCGGAATTTCAACTGAAGTTGAAGGTGCCTTTACGATCA\n+ATCATTATCTTAATCTAGCACAGCATGATTACGCGGATGAGAAGTTACGAATTAAGTCGG\n+CATGTCGTAATTGGTTTGCACAAGCATTGAGTAAACTAGACGTCATAGCTTACCCAGTTT\n+ATAACAATCAGCTCGAGATCATCGACCTAAAGTATGTACATGGTAAAGAGCCAAAGTATG\n+TAAGCACATTACATGAAAAAGTTGCCGAATCACGTCAACGTAAGCTGTCAAAATACCCAT\n+ACTTACTGGAATATATTGATAGGTCACGTAAAGCGAAAACGGTGGAGGAATTAATCCATA\n+GACTTTTAGTGATGAATGCACTTTCAAACGACCGCTCTTTCTATAAAACACGGACGGAAT\n+TATCATTAGACGCGGCGGTAAAATCAGAGGTGCGAGAGCACTTAGTTAGTGCTCCGGTCG\n+CTAAATTGATTGACCCTCAGTCTAATCGAATCTATCAGAAGTACTTTATTAGAGAAAGGA\n+ATGAAGCAATGTACTATGCTCAACAGTACTTATTAAGCTTTGTCCCAGCATTGATCCAAC\n+AACTGAGCAAAACCAACTTTGATGAGGAATGGTTACGATTTTTAACCACATCTTCACCTG\n+GAGTCAAATTACCTCAAGAAACGCTAGACAGCCTGAGTAAAACATCTGCAGTATTATCGA\n+AATCAAGACGAGGTTTGGAAGCGCTTGAAGCATCTGAATATAGAAGCATCAATCGTGTTG\n+AACGAGCGTTAGAGATGGTACTCAAATTAGTTCAAAGACAACAAAATGATAGAAGACAAC\n+GAGCGATAGCAGGCGAACCAAATTCCATTCTATTACTGACCCTTGTTTATTATGTTATCT\n+TATCGGCTATGTACGCCATGTCGACAGATGCAGCTCAAGGTAAACAGGTTGGTAATTCAA\n+TGGACCTTCAAGACTTGTTATTCGCGACAACTCAGACGGACACGCTTGTGTCATCAATTG\n+ATATTGTAGGTATGGATGCTTCTGTGCAGTCAATAACTACTGAGTTGTCAAATATTATCT\n+GTCTTGAAGTGACGCGTGGTTTACCTGAATCACAAATTGGACCATTTACAGGCGGTATGA\n+AGCGTCTTCTGCAACTAAGTGATGAACCTGGTGGAGCGTGGAAGCAGGTTGAGATGTATG\n+TATCAGGTACACTTGAGGCCGTGGTATTCGAAGGTAGTCATGCACTAACATCAACTACTT\n+ACGAGAGTAAGATTTTTGGAAGTGTTAAGAACTATGCGGGTACGTATCCCTCAGGTAGAG\n+CTGACACGTCGTCACATCACACTAAGGTTTTGGAAGGTGCGACCCGTGGTAATGAAATGC\n+GAAGAAGAACGGATGAGCGAATCGTGCACCATGCGTCGACGATTGTAATGTCACGTAATA\n+TGGGTGATGATAAGTCAGACGTATACACAGGATCATTTCCAAATGTTATATCACAATTAG\n+TGAGCGATAAAGATGTACTCGCACAATTGGGTTTTAAGACAGATGCAGATCTCTCGAGTC\n+ACAACGGAGAATTCTTGCAACAACATGTATGTAGAGGAAGGCTAGTCGGAAAACCATCAC\n+GTATATCAATAGGCACAGTAGAGCATCGTAAAGAGAAGGTTCGGATGCATGAAGCATGTC\n+AAGAACTTCTATCTATTATGGATGACCTAATTGTGCGTATTAGAGATACCGAGGGCTTGA\n+AGATGATGATCTTCTCGTTTGCTATACATTGCATTAATAGTATTGTATTAAACATTGCGA\n+AAGTTGATCTTGCCGCTATAATATCGAAATTGACTTCAAATAATTTGCGTACATATGTAT\n+ATCCTACGAAAGATGAACATGCTTTTCAGCTCGTTAGATTGTATTTTCCATTGATGTGGT\n+TCTTTATGCATAAAGGTGGTGAATTACCAGCTTATCCAATTGAACGGGTTGATGGTACTT\n+ATACAGATGACGAGTCGGTGTACACTGTGCGAGGTGAATACAAACGAAGATTGATGTTTG\n+ATATTATAGGTATTGATAAAATTGAGAAATTTGGTGACGCCATTTTCAGAAATAATCACT\n+GCTTTGATATCGGTTTGAACGCTGCTGATGCCATCATTAAGCTGAAGATAACGGATCTAC\n+CGAAGGAAATGAGAAGTGAAACGCTCGAGCATGGTATCATATCAAATCTAGCGAAAAATT\n+TAGAGTCATTCGGCAATGCTATGTCTAAGGAAGCTTCACTTCAAGCGAAACTCAGGATTG\n+AAAATGAACTTGCAGGTGTTAGGAGCGTAACTCAGACAAATGAAGTTGTCGTTGGAAGAG\n+GAAAGATAGCAAAAGTCCCAAAAAGTATTGTATACGCACATCGAACTGAAGCACAACTTG\n+AACAGATATTAATGACAAGAGAGTCGGATAATGAAGAGCGACCAATGATATCAAAGCGAA\n+TGCTTGATCACATCGCTTCACTATCGTTTCATCATGTTGTTAATGTCAAGACAACGGATA\n+AGTTACACTTGTATTACTTCTATCCTAGTGGCGATGCCCTAGTTTACGGTAATCATGCAA\n+AATACACTGAACATTTCGAATTAGCTCCACCTATGTGGTATTTGTCACCTTCATGGCGTT\n+TATATGGCCTATTAGGTACAGCGTCACAGACACGTGGTGACTTACTTCGACAAATTAATT\n+GGCTAAAAGGTAAATATGGAACGTTTAAGCTTGATGACGAGAAGATCCGTTATGGATATG\n+ATGTTATCTGGCGAAAGAACAGACATCTGCTTAATGACTACATGACAATGATCGGAGCAT\n+CACCACATCTTGAAAACTTGCTTAAGAGCATCTTTCGTTTGATGGATAGATGGGGTACTT\n+ATCGTTATGATTACATTCAAACACCGAGGAATATTTTCTTTATCTCAGACAATCCATTAG\n+TCGCTGAACAGAACATTATCTTCGCTGCAGATGGTGACGAGATAACTAGGCCCTTACAGG\n+TAATTGTCGGCTATCTACATATACTTGCGCAT\n+>gi|123840414|sp|Q2Y0E9.1|RDRP_APRVF_RecName:_Full_RNA-directed_RNA_polymerase_VP2--Locus_27_Transcript_2/7_Confidence_0.333_Length_3860_hit1_IdMatch=25.16,AligLength=1220,E-val=1e-82\n+TTATAGTACCTCAGAGTATTTTGAAGCCACCACCTTTCAAC'..b'GTGATGACAATCTACTTA\n+ACATCTCGGAAGGGGTAATTGATATCTTCAACCAACTTACCATCTCGGAAGCCATGCGTT\n+GGATAGGACACGAATACACAGATGAAACGAAAACAGGCGAGGCTGCGCCCTATCGGACAT\n+TGGAAGAAGTCCGTTTCCTTAAAAGAGGGTTCAGAATGGATCACCTCTTGTGTCGGTGGG\n+TAGCTCCTTTGAAGAAGGATGTCATCTACGAAATGCTTAATTGGACGCGCAAAGGGATTA\n+ACCCAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACG\n+GAAGGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTG\n+AATATCCTCAA\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_63_Transcript_2/2_Confidence_0.333_Length_343_hit1_IdMatch=54.37,AligLength=103,E-val=5e-27\n+TAGGACACGAATACACAGATGAAACGAAAACAGGCGAGGCTGCGCCCTATCGGACATTGG\n+AAGAAGTCCGTTTCCTTAAAAGAGGGTTCAGAATGGATCACCTCTTGTGTCGGTGGGTAG\n+CTCCTTTGAAGAAGGATGTCATCTACGAAATGCTTAATTGGACGCGCAAAGGGATTAACC\n+CAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACGGAA\n+GGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTGAAT\n+ATCCTCAA\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=46.44,AligLength=450,E-val=8e-138\n+TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC\n+TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA\n+TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG\n+CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG\n+CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG\n+TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT\n+GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT\n+TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC\n+TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG\n+CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT\n+TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT\n+ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG\n+TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA\n+AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG\n+GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG\n+GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG\n+GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG\n+TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC\n+TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA\n+CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC\n+GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG\n+GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC\n+TCGATGTGTACGAATTCGTGCGC\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_2/2_Confidence_0.333_Length_1324_hit1_IdMatch=46.74,AligLength=445,E-val=1e-135\n+CTTGAGGATACTTTACCAGGTATGGTCGAGCACGTTACGCTCGTAGCACAAAATACATCC\n+GCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAATGCTTTGCATTGTTTTGATT\n+TGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCGCGGTACTTATAGTGGTTGCT\n+CTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAGCTATGGACATGTATCGCGTA\n+ATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCGTTTTCCATCCGTGGTTGAAC\n+ACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGTGTCTCAAGAAATTACCAGGA\n+AAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCTTACCCAAAGCTGTTAAGGGT\n+GCGACACAACTACATGAATGGGTGTCAAAATACTTCGATCTCTCTTTGGATCACGTCAAG\n+GCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGGCTGAATCATCAAGCGCCAAA\n+GTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGATTGGAACAACGAAGTAAAATC\n+GATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGTATCACACTGGATTGCAATTT\n+GCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCGTGAACAGTGCGCTAAGACCA\n+GCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAAAAGGAGGGAGTCGTAAGATG\n+AGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTGGGAAAACCTCTATGGTGGAT\n+CCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGGGACCTGAACATCTCCACTCG\n+TTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATGGTTACAAAGCCCACAAGATA\n+GTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTGTGAACAGGAATTTGGAGGTA\n+TTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACCTTCATATGGCTTGTCTCTCG\n+GATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACACTACCAACGAAATGAATGTC\n+AAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACCGCATGAGTGAAAACGCGTTC\n+ACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAGGATCAACCGGCAATAAGCAG\n+TATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATCTCGATGTGTACGAATTCGTG\n+CGC\n' |
| b |
| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/output_exact.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_exact.fa Fri May 21 09:34:14 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +>gi|81971654|sp|Q9IJX4.1|POLN_CRPVC_RecName:_Full_Replicase_polyprotein;_Contains:_RecName:_Full_Pro--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=43.46,AligLength=451,E-val=2e-122 +TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC +TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA +TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG +CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG +CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG +TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT +GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT +TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC +TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG +CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT +TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT +ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG +TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA +AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG +GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG +GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG +GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG +TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC +TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA +CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC +GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG +GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC +TCGATGTGTACGAATTCGTGCGC |
| b |
| diff -r 321cad0eb507 -r c282a8a47dd9 test-data/output_exactly_not.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_exactly_not.fa Fri May 21 09:34:14 2021 +0000 |
| b |
| b'@@ -0,0 +1,5881 @@\n+>gi|123840414|sp|Q2Y0E9.1|RDRP_APRVF_RecName:_Full_RNA-directed_RNA_polymerase_VP2--Locus_27_Transcript_1/7_Confidence_0.444_Length_3872_hit1_IdMatch=25.16,AligLength=1220,E-val=1e-82\n+TTATAGTACCTCAGAGTATTTTGAAGCCACCACCTTTCAACGAGAAAGACTGGCCTTTGA\n+ATGAAGACGAGAGTATGTTCAGTGCCTCGCGCAAGTATAATTACATGATAAATACTAGTA\n+CGTTGAGCCTTTATGGTTCGAGGGAAAGTTTAGTCGGTAAAGCAATATACGGTTTATATA\n+CTGATGAGCAATCACAGTCACGCTTCAGGACAGTATGGCATCAAATAATGGCAAGTGTCT\n+ACGCACTAGACGATTATCTAGGTCATACTAACCATCCAGTTCGTGCAGTGTTGGCACAGT\n+TAAACTTAGACAAAGGATTACCATTCAAGGAAACTGCTGAAGGTATTGACTTAACAGAGG\n+CGGTTGAAAAAGGAATTGATTCGAGTACATTACTACCATCAATATTATATATGTTGATCT\n+CAGTATCGTGCGATATCTGTTTCGGAATTTCAACTGAAGTTGAAGGTGCCTTTACGATCA\n+ATCATTATCTTAATCTAGCACAGCATGATTACGCGGATGAGAAGTTACGAATTAAGTCGG\n+CATGTCGTAATTGGTTTGCACAAGCATTGAGTAAACTAGACGTCATAGCTTACCCAGTTT\n+ATAACAATCAGCTCGAGATCATCGACCTAAAGTATGTACATGGTAAAGAGCCAAAGTATG\n+TAAGCACATTACATGAAAAAGTTGCCGAATCACGTCAACGTAAGCTGTCAAAATACCCAT\n+ACTTACTGGAATATATTGATAGGTCACGTAAAGCGAAAACGGTGGAGGAATTAATCCATA\n+GACTTTTAGTGATGAATGCACTTTCAAACGACCGCTCTTTCTATAAAACACGGACGGAAT\n+TATCATTAGACGCGGCGGTAAAATCAGAGGTGCGAGAGCACTTAGTTAGTGCTCCGGTCG\n+CTAAATTGATTGACCCTCAGTCTAATCGAATCTATCAGAAGTACTTTATTAGAGAAAGGA\n+ATGAAGCAATGTACTATGCTCAACAGTACTTATTAAGCTTTGTCCCAGCATTGATCCAAC\n+AACTGAGCAAAACCAACTTTGATGAGGAATGGTTACGATTTTTAACCACATCTTCACCTG\n+GAGTCAAATTACCTCAAGAAACGCTAGACAGCCTGAGTAAAACATCTGCAGTATTATCGA\n+AATCAAGACGAGGTTTGGAAGCGCTTGAAGCATCTGAATATAGAAGCATCAATCGTGTTG\n+AACGAGCGTTAGAGATGGTACTCAAATTAGTTCAAAGACAACAAAATGATAGAAGACAAC\n+GAGCGATAGCAGGCGAACCAAATTCCATTCTATTACTGACCCTTGTTTATTATGTTATCT\n+TATCGGCTATGTACGCCATGTCGACAGATGCAGCTCAAGGTAAACAGGTTGGTAATTCAA\n+TGGACCTTCAAGACTTGTTATTCGCGACAACTCAGACGGACACGCTTGTGTCATCAATTG\n+ATATTGTAGGTATGGATGCTTCTGTGCAGTCAATAACTACTGAGTTGTCAAATATTATCT\n+GTCTTGAAGTGACGCGTGGTTTACCTGAATCACAAATTGGACCATTTACAGGCGGTATGA\n+AGCGTCTTCTGCAACTAAGTGATGAACCTGGTGGAGCGTGGAAGCAGGTTGAGATGTATG\n+TATCAGGTACACTTGAGGCCGTGGTATTCGAAGGTAGTCATGCACTAACATCAACTACTT\n+ACGAGAGTAAGATTTTTGGAAGTGTTAAGAACTATGCGGGTACGTATCCCTCAGGTAGAG\n+CTGACACGTCGTCACATCACACTAAGGTTTTGGAAGGTGCGACCCGTGGTAATGAAATGC\n+GAAGAAGAACGGATGAGCGAATCGTGCACCATGCGTCGACGATTGTAATGTCACGTAATA\n+TGGGTGATGATAAGTCAGACGTATACACAGGATCATTTCCAAATGTTATATCACAATTAG\n+TGAGCGATAAAGATGTACTCGCACAATTGGGTTTTAAGACAGATGCAGATCTCTCGAGTC\n+ACAACGGAGAATTCTTGCAACAACATGTATGTAGAGGAAGGCTAGTCGGAAAACCATCAC\n+GTATATCAATAGGCACAGTAGAGCATCGTAAAGAGAAGGTTCGGATGCATGAAGCATGTC\n+AAGAACTTCTATCTATTATGGATGACCTAATTGTGCGTATTAGAGATACCGAGGGCTTGA\n+AGATGATGATCTTCTCGTTTGCTATACATTGCATTAATAGTATTGTATTAAACATTGCGA\n+AAGTTGATCTTGCCGCTATAATATCGAAATTGACTTCAAATAATTTGCGTACATATGTAT\n+ATCCTACGAAAGATGAACATGCTTTTCAGCTCGTTAGATTGTATTTTCCATTGATGTGGT\n+TCTTTATGCATAAAGGTGGTGAATTACCAGCTTATCCAATTGAACGGGTTGATGGTACTT\n+ATACAGATGACGAGTCGGTGTACACTGTGCGAGGTGAATACAAACGAAGATTGATGTTTG\n+ATATTATAGGTATTGATAAAATTGAGAAATTTGGTGACGCCATTTTCAGAAATAATCACT\n+GCTTTGATATCGGTTTGAACGCTGCTGATGCCATCATTAAGCTGAAGATAACGGATCTAC\n+CGAAGGAAATGAGAAGTGAAACGCTCGAGCATGGTATCATATCAAATCTAGCGAAAAATT\n+TAGAGTCATTCGGCAATGCTATGTCTAAGGAAGCTTCACTTCAAGCGAAACTCAGGATTG\n+AAAATGAACTTGCAGGTGTTAGGAGCGTAACTCAGACAAATGAAGTTGTCGTTGGAAGAG\n+GAAAGATAGCAAAAGTCCCAAAAAGTATTGTATACGCACATCGAACTGAAGCACAACTTG\n+AACAGATATTAATGACAAGAGAGTCGGATAATGAAGAGCGACCAATGATATCAAAGCGAA\n+TGCTTGATCACATCGCTTCACTATCGTTTCATCATGTTGTTAATGTCAAGACAACGGATA\n+AGTTACACTTGTATTACTTCTATCCTAGTGGCGATGCCCTAGTTTACGGTAATCATGCAA\n+AATACACTGAACATTTCGAATTAGCTCCACCTATGTGGTATTTGTCACCTTCATGGCGTT\n+TATATGGCCTATTAGGTACAGCGTCACAGACACGTGGTGACTTACTTCGACAAATTAATT\n+GGCTAAAAGGTAAATATGGAACGTTTAAGCTTGATGACGAGAAGATCCGTTATGGATATG\n+ATGTTATCTGGCGAAAGAACAGACATCTGCTTAATGACTACATGACAATGATCGGAGCAT\n+CACCACATCTTGAAAACTTGCTTAAGAGCATCTTTCGTTTGATGGATAGATGGGGTACTT\n+ATCGTTATGATTACATTCAAACACCGAGGAATATTTTCTTTATCTCAGACAATCCATTAG\n+TCGCTGAACAGAACATTATCTTCGCTGCAGATGGTGACGAGATAACTAGGCCCTTACAGG\n+TAATTGTCGGCTATCTACATATACTTGCGCAT\n+>gi|123840414|sp|Q2Y0E9.1|RDRP_APRVF_RecName:_Full_RNA-directed_RNA_polymerase_VP2--Locus_27_Transcript_2/7_Confidence_0.333_Length_3860_hit1_IdMatch=25.16,AligLength=1220,E-val=1e-82\n+TTATAGTACCTCAGAGTATTTTGAAGCCACCACCTTTCAAC'..b'GTGATGACAATCTACTTA\n+ACATCTCGGAAGGGGTAATTGATATCTTCAACCAACTTACCATCTCGGAAGCCATGCGTT\n+GGATAGGACACGAATACACAGATGAAACGAAAACAGGCGAGGCTGCGCCCTATCGGACAT\n+TGGAAGAAGTCCGTTTCCTTAAAAGAGGGTTCAGAATGGATCACCTCTTGTGTCGGTGGG\n+TAGCTCCTTTGAAGAAGGATGTCATCTACGAAATGCTTAATTGGACGCGCAAAGGGATTA\n+ACCCAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACG\n+GAAGGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTG\n+AATATCCTCAA\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_63_Transcript_2/2_Confidence_0.333_Length_343_hit1_IdMatch=54.37,AligLength=103,E-val=5e-27\n+TAGGACACGAATACACAGATGAAACGAAAACAGGCGAGGCTGCGCCCTATCGGACATTGG\n+AAGAAGTCCGTTTCCTTAAAAGAGGGTTCAGAATGGATCACCTCTTGTGTCGGTGGGTAG\n+CTCCTTTGAAGAAGGATGTCATCTACGAAATGCTTAATTGGACGCGCAAAGGGATTAACC\n+CAGATGATGTGACGATGATGATCATTGATACAGCATTTAGGGAGATCTCTTATCACGGAA\n+GGGAAGCTTTCGAGAAGCTGCGAGGGCAGATACTTGAGCAGCGGGATGTGTTGGTTGAAT\n+ATCCTCAA\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_1/2_Confidence_0.667_Length_1344_hit1_IdMatch=46.44,AligLength=450,E-val=8e-138\n+TAGATAAGGTTTGCTCATTTCTTGAGGATGCTTTACCAGGTATGGTCGAGCACGTTACGC\n+TCGTAGCACAAAATACATCCGCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAA\n+TGCTTTGCATTGTTTTGATTTGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCG\n+CGGTACTTATAGTGGTTGCTCTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAG\n+CTATGGACATGTATCGCGTAATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCG\n+TTTTCCATCCGTGGTTGAACACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGT\n+GTCTCAAGAAATTACCAGGAAAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCT\n+TACCCAAAGCTGTTAAGGGTGCGACACAACTACATGAATGGGTGTCAAAATACTTCGATC\n+TCTCTTTGGATCACGTCAAGGCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGG\n+CTGAATCATCAAGCGCCAAAGTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGAT\n+TGGAACAACGAAGTAAAATCGATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGT\n+ATCACACTGGATTGCAATTTGCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCG\n+TGAACAGTGCGCTAAGACCAGCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAA\n+AAGGAGGGAGTCGTAAGATGAGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTG\n+GGAAAACCTCTATGGTGGATCCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGG\n+GACCTGAACATCTCCACTCGTTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATG\n+GTTACAAAGCCCACAAGATAGTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTG\n+TGAACAGGAATTTGGAGGTATTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACC\n+TTCATATGGCTTGTCTCTCGGATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACA\n+CTACCAACGAAATGAATGTCAAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACC\n+GCATGAGTGAAAACGCGTTCACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAG\n+GATCAACCGGCAATAAGCAGTATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATC\n+TCGATGTGTACGAATTCGTGCGC\n+>gi|9629651|ref|NP_044945.1|_replicase_polyprotein__Drosophila_C_virus--Locus_65_Transcript_2/2_Confidence_0.333_Length_1324_hit1_IdMatch=46.74,AligLength=445,E-val=1e-135\n+CTTGAGGATACTTTACCAGGTATGGTCGAGCACGTTACGCTCGTAGCACAAAATACATCC\n+GCGTCAGCCAAGGTGTTATCTGACGAGTTGATCAAATCAATGCTTTGCATTGTTTTGATT\n+TGCTTGTTGATTGAAACCAAGTTCTATAAGACCGCTTTCGCGGTACTTATAGTGGTTGCT\n+CTACGTGTTTTCGGGTACAGTGAGCAAATAATTGAGACAGCTATGGACATGTATCGCGTA\n+ATTAGGGCTCCAAAGGCTCAAGGTAATATGGAAGATGTCGTTTTCCATCCGTGGTTGAAC\n+ACGTGTGGAAAGTTGATTTTCCTACTTATCGCTGTCCTGTGTCTCAAGAAATTACCAGGA\n+AAGAACGACGTAGACACTTTCATGCGCAGGCTCGACAGCTTACCCAAAGCTGTTAAGGGT\n+GCGACACAACTACATGAATGGGTGTCAAAATACTTCGATCTCTCTTTGGATCACGTCAAG\n+GCGATGATTGTTGGTAAATCTTGTGCCGAAATGAAGAAGGCTGAATCATCAAGCGCCAAA\n+GTTTTGGCTTGGGCCGCTAGAGTTCAAGATTTCGTCAGATTGGAACAACGAAGTAAAATC\n+GATAGTGATATCGCTGTCGCCAACGAGGCTGAAGCCTTGTATCACACTGGATTGCAATTT\n+GCAGGAGACACTCTGTTACCTCCAGAATTGCACAAGGTCGTGAACAGTGCGCTAAGACCA\n+GCCCGCGATATATATGAGTACGTCACCCGCTCCCCAATAAAAGGAGGGAGTCGTAAGATG\n+AGACCCTTGATGATTTGGCTAGCTGGCCAGTCAGGAATTGGGAAAACCTCTATGGTGGAT\n+CCTCTATGTATCGATTTGCTTCGAGCAATGGGTTATGTGGGACCTGAACATCTCCACTCG\n+TTGGTGTATGGCCGCCAAGTTGAGACGGAGTACTGGGATGGTTACAAAGCCCACAAGATA\n+GTGATCTATGATGATGCTTTTCAGCTGAAAGATGATGCTGTGAACAGGAATTTGGAGGTA\n+TTTGAGGTTATACGTTCTTGCAACACGTATCCTCAACACCTTCATATGGCTTGTCTCTCG\n+GATAAAAACACTTTTTCAGTAGCGGAAGTGTACATCTACACTACCAACGAAATGAATGTC\n+AAACTTGAGTCGCTGACTCATGAACAAGCATTCTACAACCGCATGAGTGAAAACGCGTTC\n+ACTGTGCGTCCAAAAGAGGCTTATCGTCTAGTCGAAGAAGGATCAACCGGCAATAAGCAG\n+TATCGTTTGGACAAAACGAAAACCAAAGGAGCTATCGATCTCGATGTGTACGAATTCGTG\n+CGC\n' |