Mercurial > repos > dfornika > match_plasmid_to_reference

annotate match_plasmid_to_reference.py @ 1:3616b6eda1da draft

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"planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
author dfornika
date Wed, 06 Nov 2019 00:42:05 -0500
parents 8bb674372911
children 826ddf832bef
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8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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1 #!/usr/bin/env python
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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3 from __future__ import print_function
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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5 import argparse
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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6 import csv
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7 import errno
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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8 import json
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9 import os
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10 import re
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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11 import shutil
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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12 import sys
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8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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14 from pprint import pprint
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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15
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16 MOB_TYPER_FIELDNAMES = [
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17 "file_id",
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18 "num_contigs",
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19 "total_length",
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20 "gc",
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21 "rep_type(s)",
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22 "rep_type_accession(s)",
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23 "relaxase_type(s)",
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24 "relaxase_type_accession(s)",
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25 "mpf_type",
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26 "mpf_type_accession(s)",
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27 "orit_type(s)",
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28 "orit_accession(s)",
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29 "PredictedMobility",
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30 "mash_nearest_neighbor",
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31 "mash_neighbor_distance",
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32 "mash_neighbor_cluster",
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33 "NCBI-HR-rank",
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34 "NCBI-HR-Name",
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35 "LitRepHRPlasmClass",
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36 "LitPredDBHRRank",
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37 "LitPredDBHRRankSciName",
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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38 "LitRepHRRankInPubs",
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39 "LitRepHRNameInPubs",
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40 "LitMeanTransferRate",
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41 "LitClosestRefAcc",
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42 "LitClosestRefDonorStrain",
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43 "LitClosestRefRecipientStrain",
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44 "LitClosestRefTransferRate",
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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45 "LitClosestConjugTemp",
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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46 "LitPMIDs",
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47 "LitPMIDsNumber",
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48 ]
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49
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50 def parse_mob_typer_report(mob_typer_report_path):
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51 mob_typer_report = []
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52
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53 with open(mob_typer_report_path) as f:
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54 reader = csv.DictReader(f, delimiter="\t", quotechar='"', fieldnames=MOB_TYPER_FIELDNAMES)
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55 for row in reader:
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56 mob_typer_report.append(row)
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57 return mob_typer_report
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59 def parse_genbank_accession(genbank_file_path):
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60 with open(genbank_file_path, 'r') as f:
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61 while True:
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62 line = f.readline()
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63 # break while statement if it is not a comment line
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64 # i.e. does not startwith #
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65 if line.startswith('ACCESSION'):
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66 return line.strip().split()[1]
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67
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69 def count_contigs(plasmid_fasta_path):
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70 contigs = 0
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71 with open(plasmid_fasta_path, 'r') as f:
1
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72 for line in f:
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73 if line.startswith('>'):
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74 contigs += 1
0
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75 return contigs
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76
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77 def count_bases(plasmid_fasta_path):
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78 bases = 0
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79 with open(plasmid_fasta_path, 'r') as f:
1
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80 for line in f:
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81 line = line.strip()
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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82 if not line.startswith('>'):
3616b6eda1da "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
dfornika
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83 bases += len(line)
0
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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84 return bases
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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85
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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86 def main(args):
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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87 # create output directory
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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88 try:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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89 os.mkdir(args.outdir)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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90 except OSError as exc:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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91 if exc.errno == errno.EEXIST and os.path.isdir(args.outdir):
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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92 pass
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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93 else:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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94 raise
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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95
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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96 # parse mob_typer report
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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97 mob_typer_report = parse_mob_typer_report(args.mob_typer_report)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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98 num_plasmid_contigs = count_contigs(args.plasmid)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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99 num_plasmid_bases = count_bases(args.plasmid)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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100
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101 with open(os.path.join(args.outdir, 'mob_typer_record.tsv'), 'w') as f:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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102 mob_typer_record_writer = csv.DictWriter(f, delimiter="\t", quotechar='"', fieldnames=MOB_TYPER_FIELDNAMES)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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103 mob_typer_record_writer.writeheader()
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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104 for record in mob_typer_report:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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105 if num_plasmid_contigs == int(record['num_contigs']) and num_plasmid_bases == int(record['total_length']):
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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106 for reference_plasmid in args.reference_plasmids:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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107 if parse_genbank_accession(reference_plasmid) == record['mash_nearest_neighbor']:
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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108 shutil.copy2(reference_plasmid, os.path.join(args.outdir, "reference_plasmid.gbk"))
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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109 mob_typer_record_writer.writerow(record)
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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110
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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111 shutil.copy2(args.plasmid, os.path.join(args.outdir, "plasmid.fasta"))
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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112
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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113
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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114 if __name__ == '__main__':
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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115 parser = argparse.ArgumentParser()
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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116 parser.add_argument("--plasmid", help="plasmid assembly (fasta)")
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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117 parser.add_argument("--reference_plasmids", nargs='+', help="reference plasmids (genbank)")
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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118 parser.add_argument("--mob_typer_report", help="mob_typer reports (tsv)")
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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119 parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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120 args = parser.parse_args()
8bb674372911 "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/match_plasmid_to_reference commit dcdac86bce5c44043516fbd472ab7c19d7bf4d50-dirty"
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121 main(args)