Mercurial > repos > artbio > cherry_pick_fasta

annotate cherry_pick_fasta.py @ 1:19a1ce11945e draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
author artbio
date Fri, 21 May 2021 09:33:44 +0000
parents ab910a0adc69
children d04b7de95782
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ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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1 #!/usr/bin/env python
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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2 # -*- coding: utf-8 -*-
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19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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3 # Chery pick of fasta sequences satisfying a query string in their header/name
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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4 import argparse
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6 from Bio import SeqIO
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ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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9 def Parser():
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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10 the_parser = argparse.ArgumentParser(
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11 description='Cherry pick fasta sequences')
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12 the_parser.add_argument('--input', action='store', type=str,
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13 help='input fasta file')
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14 the_parser.add_argument('--searchfor', action='store', type=str,
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15 help='with, without, or withlist, withoutlist')
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16 the_parser.add_argument('--mode', action='store', type=str,
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17 default='includes', help='exact or includes')
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18 the_parser.add_argument('--query-string', dest='query_string',
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19 action='store', type=str,
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20 help='headers containing the string will be \
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21 extracted or excluded as well as the \
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22 corresponding sequence')
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23 the_parser.add_argument('--query-file', dest='query_file',
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24 action='store', type=str,
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25 help='headers containing any of the strings \
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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26 provided in the text file (1 string per \
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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27 line) will be extracted or excluded as well \
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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28 as the corresponding sequence')
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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29 the_parser.add_argument('--output', action='store', type=str,
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30 help='output fasta file')
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31 args = the_parser.parse_args()
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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32 return args
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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34
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35 def parse_fasta_dict(query, fasta_dict, mode):
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36 if not isinstance(query, list):
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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37 query = [query]
ab910a0adc69 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit f527add7e7bace30b8bc67524ff1da1bf920ec29"
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38 accumulator = []
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19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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39 if mode == 'includes':
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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40 for seq_id in fasta_dict:
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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41 for string in query:
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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42 if string in seq_id:
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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43 accumulator.append(seq_id)
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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44 continue
19a1ce11945e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit d637de6c1090314bd34bdffc2fdf979cb55b870b"
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45 elif mode == 'exact':
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46 for seq_id in fasta_dict:
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47 for string in query:
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48 if string == seq_id:
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49 accumulator.append(seq_id)
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50 continue
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51 res_dict = {k: fasta_dict[k] for k in fasta_dict if k in accumulator}
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52 return res_dict
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55 def complement_fasta_dict(fasta_dict, subfasta_dict):
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56 fasta_ids = list(fasta_dict.keys())
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57 subfasta_ids = list(subfasta_dict.keys())
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58 complement_ids = list(set(fasta_ids) - set(subfasta_ids))
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59 sub_dict = {k: fasta_dict[k] for k in fasta_dict if k in complement_ids}
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60 return sub_dict
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63 def getquerylist(file):
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64 querylist = []
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65 for line in open(file, 'r'):
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66 querylist.append(line.rstrip())
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67 return querylist
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70 def buid_fasta_dict(fasta):
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71 seq_dict = {rec.id: rec.seq for rec in SeqIO.parse(fasta, "fasta")}
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72 return seq_dict
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75 def write_fasta_result(fasta_dict, file):
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76 line_length = 60
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77 with open(file, 'w') as f:
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78 for header in sorted(fasta_dict):
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79 f.write('>%s\n' % header)
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80 for i in range(line_length, len(fasta_dict[header]), line_length):
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81 f.write('%s\n' % fasta_dict[header][i-line_length:i])
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82 f.write('%s\n' % fasta_dict[header][i:])
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84
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85 def __main__():
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86 ''' main function '''
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87 args = Parser()
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88 fasta_dict = buid_fasta_dict(args.input)
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89 if args.query_string:
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90 query = args.query_string
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91 elif args.query_file:
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92 query = getquerylist(args.query_file)
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93 if args.searchfor == 'with':
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94 fasta_result_dict = parse_fasta_dict(query, fasta_dict, args.mode)
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95 elif args.searchfor == 'without':
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96 fasta_result_dict = complement_fasta_dict(fasta_dict, parse_fasta_dict(
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97 query, fasta_dict,
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98 args.mode))
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99 write_fasta_result(fasta_result_dict, args.output)
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100
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101
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102 if __name__ == '__main__':
0
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103 __main__()