Mercurial > repos > iss > eurl_vtec_wgs_pt
annotate scripts/ReMatCh/utils/convert_Ns_to_gaps.py @ 0:c6bab5103a14 draft
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author | iss |
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date | Mon, 21 Mar 2022 15:23:09 +0000 |
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1 #!/usr/bin/env python3 |
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2 |
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3 # -*- coding: utf-8 -*- |
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4 |
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5 """ |
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6 convert_Ns_to_gaps.py - Convert the Ns into gaps |
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7 <https://github.com/B-UMMI/ReMatCh/> |
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8 |
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9 Copyright (C) 2018 Miguel Machado <mpmachado@medicina.ulisboa.pt> |
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10 |
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11 Last modified: October 15, 2018 |
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12 |
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13 This program is free software: you can redistribute it and/or modify |
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14 it under the terms of the GNU General Public License as published by |
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15 the Free Software Foundation, either version 3 of the License, or |
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16 (at your option) any later version. |
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17 |
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18 This program is distributed in the hope that it will be useful, |
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19 but WITHOUT ANY WARRANTY; without even the implied warranty of |
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20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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21 GNU General Public License for more details. |
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22 |
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23 You should have received a copy of the GNU General Public License |
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24 along with this program. If not, see <http://www.gnu.org/licenses/>. |
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25 """ |
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26 |
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27 import os |
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28 import argparse |
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29 |
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30 |
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31 version = '0.2' |
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32 |
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33 |
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34 def conversion(infile, outfile): |
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35 last_printed = 0 |
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36 counter = 1 |
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37 with open(infile, 'rtU') as reader: |
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38 with open(outfile, 'wt') as writer: |
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39 for line in reader: |
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40 line = line.rstrip('\r\n') |
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41 if line.startswith('>'): |
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42 writer.write(line + '\n') |
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43 if counter % 10 == 0: |
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44 print('\n' + str(counter) + ' sequences already processed') |
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45 last_printed = counter |
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46 counter += 1 |
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47 else: |
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48 if len(line) > 0: |
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49 line = line.replace('N', '-') |
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50 writer.write(line + '\n') |
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51 if last_printed < counter: |
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52 print('\n' + str(counter - 1) + ' sequences already processed') |
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53 |
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54 |
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55 def convert_n_2_gaps(args): |
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56 outdir = os.path.dirname(os.path.abspath(args.outfile)) |
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57 if not os.path.isdir(outdir): |
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58 os.makedirs(outdir) |
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59 |
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60 outfile = os.path.abspath(args.outfile) |
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61 |
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62 infile = os.path.abspath(args.infile.name) |
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63 |
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64 conversion(infile, outfile) |
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65 |
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66 |
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67 def main(): |
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68 parser = argparse.ArgumentParser(prog='convert_Ns_to_gaps.py', description='Convert the Ns into gaps', |
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69 formatter_class=argparse.ArgumentDefaultsHelpFormatter) |
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70 parser.add_argument('--version', help='Version information', action='version', version=str('%(prog)s v' + version)) |
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71 |
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72 parser_required = parser.add_argument_group('Required options') |
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73 parser_required.add_argument('-i', '--infile', type=argparse.FileType('r'), metavar='/path/to/input/file.fasta', |
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74 help='Path to the fasta file', required=True) |
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75 parser_required.add_argument('-o', '--outfile', type=str, metavar='/path/to/converted/output/file.fasta', |
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76 help='Converted output fasta file', required=True, |
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77 default='converted_Ns_to_gaps.fasta') |
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78 |
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79 args = parser.parse_args() |
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80 |
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81 convert_n_2_gaps(args) |
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82 |
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83 |
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84 if __name__ == "__main__": |
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85 main() |