Mercurial > repos > computational-metabolomics > metfrag
annotate metfrag.py @ 0:fd5c0b39569a draft
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
author | computational-metabolomics |
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date | Wed, 05 Feb 2020 12:30:06 -0500 |
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children | 9ee2e2ceb2c9 |
rev | line source |
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0
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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1 from __future__ import absolute_import, print_function |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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2 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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3 import ConfigParser |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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4 import argparse |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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5 import csv |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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6 import glob |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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7 import multiprocessing |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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8 import os |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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9 import re |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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10 import shutil |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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11 import sys |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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12 import tempfile |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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13 from collections import defaultdict |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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14 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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15 import six |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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16 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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17 print(sys.version) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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18 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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19 parser = argparse.ArgumentParser() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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20 parser.add_argument('--input_pth') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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21 parser.add_argument('--result_pth', default='metfrag_result.csv') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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22 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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23 parser.add_argument('--temp_dir') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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24 parser.add_argument('--polarity', default='pos') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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25 parser.add_argument('--minMSMSpeaks', default=1) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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26 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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27 parser.add_argument('--MetFragDatabaseType', default='PubChem') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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28 parser.add_argument('--LocalDatabasePath', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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29 parser.add_argument('--LocalMetChemDatabaseServerIp', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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30 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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31 parser.add_argument('--DatabaseSearchRelativeMassDeviation', default=5) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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32 parser.add_argument('--FragmentPeakMatchRelativeMassDeviation', default=10) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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33 parser.add_argument('--FragmentPeakMatchAbsoluteMassDeviation', default=0.001) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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34 parser.add_argument('--NumberThreads', default=1) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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35 parser.add_argument('--UnconnectedCompoundFilter', action='store_true') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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36 parser.add_argument('--IsotopeFilter', action='store_true') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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37 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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38 parser.add_argument('--FilterMinimumElements', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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39 parser.add_argument('--FilterMaximumElements', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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40 parser.add_argument('--FilterSmartsInclusionList', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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41 parser.add_argument('--FilterSmartsExclusionList', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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42 parser.add_argument('--FilterIncludedElements', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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43 parser.add_argument('--FilterExcludedElements', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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44 parser.add_argument('--FilterIncludedExclusiveElements', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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45 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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46 parser.add_argument('--score_thrshld', default=0) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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47 parser.add_argument('--pctexplpeak_thrshld', default=0) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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48 parser.add_argument('--schema') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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49 parser.add_argument('--cores_top_level', default=1) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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50 parser.add_argument('--chunks', default=1) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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51 parser.add_argument('--meta_select_col', default='name') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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52 parser.add_argument('--skip_invalid_adducts', action='store_true') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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53 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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54 parser.add_argument('--ScoreSuspectLists', default='') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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55 parser.add_argument('--MetFragScoreTypes', |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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56 default="FragmenterScore,OfflineMetFusionScore") |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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57 parser.add_argument('--MetFragScoreWeights', default="1.0,1.0") |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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58 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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59 args = parser.parse_args() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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60 print(args) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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61 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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62 config = ConfigParser.ConfigParser() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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63 config.read( |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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64 os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.ini')) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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65 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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66 if os.stat(args.input_pth).st_size == 0: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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67 print('Input file empty') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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68 exit() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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69 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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70 # Create temporary working directory |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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71 if args.temp_dir: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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72 wd = args.temp_dir |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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73 else: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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74 wd = tempfile.mkdtemp() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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75 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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76 if os.path.exists(wd): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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77 shutil.rmtree(wd) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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78 os.makedirs(wd) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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79 else: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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80 os.makedirs(wd) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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81 |
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"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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82 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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83 # Setup regular expressions for MSP parsing dictionary |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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84 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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85 regex_msp = {} |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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86 regex_msp['name'] = [r'^Name(?:=|:)(.*)$'] |
fd5c0b39569a
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87 regex_msp['polarity'] = [r'^ion.*mode(?:=|:)(.*)$', |
fd5c0b39569a
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88 r'^ionization.*mode(?:=|:)(.*)$', |
fd5c0b39569a
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89 r'^polarity(?:=|:)(.*)$'] |
fd5c0b39569a
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90 regex_msp['precursor_mz'] = [r'^precursor.*m/z(?:=|:)\s*(\d*[.,]?\d*)$', |
fd5c0b39569a
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91 r'^precursor.*mz(?:=|:)\s*(\d*[.,]?\d*)$'] |
fd5c0b39569a
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92 regex_msp['precursor_type'] = [r'^precursor.*type(?:=|:)(.*)$', |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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93 r'^adduct(?:=|:)(.*)$', |
fd5c0b39569a
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94 r'^ADDUCTIONNAME(?:=|:)(.*)$'] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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95 regex_msp['num_peaks'] = [r'^Num.*Peaks(?:=|:)\s*(\d*)$'] |
fd5c0b39569a
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96 regex_msp['msp'] = [r'^Name(?:=|:)(.*)$'] # Flag for standard MSP format |
fd5c0b39569a
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97 |
fd5c0b39569a
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98 regex_massbank = {} |
fd5c0b39569a
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99 regex_massbank['name'] = [r'^RECORD_TITLE:(.*)$'] |
fd5c0b39569a
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100 regex_massbank['polarity'] = [r'^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$'] |
fd5c0b39569a
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101 regex_massbank['precursor_mz'] = [ |
fd5c0b39569a
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102 r'^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d*[.,]?\d*)$'] |
fd5c0b39569a
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103 regex_massbank['precursor_type'] = [ |
fd5c0b39569a
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104 r'^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$'] |
fd5c0b39569a
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105 regex_massbank['num_peaks'] = [r'^PK\$NUM_PEAK:\s+(\d*)'] |
fd5c0b39569a
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106 regex_massbank['cols'] = [r'^PK\$PEAK:\s+(.*)'] |
fd5c0b39569a
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107 regex_massbank['massbank'] = [ |
fd5c0b39569a
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108 r'^RECORD_TITLE:(.*)$'] # Flag for massbank format |
fd5c0b39569a
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109 |
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110 if args.schema == 'msp': |
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111 meta_regex = regex_msp |
fd5c0b39569a
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112 elif args.schema == 'massbank': |
fd5c0b39569a
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113 meta_regex = regex_massbank |
fd5c0b39569a
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114 elif args.schema == 'auto': |
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115 # If auto we just check for all the available paramter names and then |
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116 # determine if Massbank or MSP based on the name parameter |
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117 meta_regex = {} |
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118 meta_regex.update(regex_massbank) |
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119 meta_regex['name'].extend(regex_msp['name']) |
fd5c0b39569a
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120 meta_regex['polarity'].extend(regex_msp['polarity']) |
fd5c0b39569a
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121 meta_regex['precursor_mz'].extend(regex_msp['precursor_mz']) |
fd5c0b39569a
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122 meta_regex['precursor_type'].extend(regex_msp['precursor_type']) |
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123 meta_regex['num_peaks'].extend(regex_msp['num_peaks']) |
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124 meta_regex['msp'] = regex_msp['msp'] |
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125 else: |
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126 sys.exit("No schema selected") |
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127 |
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128 adduct_types = { |
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129 '[M+H]+': 1.007276, |
fd5c0b39569a
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130 '[M+NH4]+': 18.034374, |
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131 '[M+Na]+': 22.989218, |
fd5c0b39569a
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132 '[M+K]+': 38.963158, |
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133 '[M+CH3OH+H]+': 33.033489, |
fd5c0b39569a
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134 '[M+ACN+H]+': 42.033823, |
fd5c0b39569a
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135 '[M+ACN+Na]+': 64.015765, |
fd5c0b39569a
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136 '[M+2ACN+H]+': 83.06037, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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137 '[M-H]-': -1.007276, |
fd5c0b39569a
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138 '[M+Cl]-': 34.969402, |
fd5c0b39569a
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139 '[M+HCOO]-': 44.99819, |
fd5c0b39569a
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140 '[M-H+HCOOH]-': 44.99819, |
fd5c0b39569a
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141 # same as above but different style of writing adduct |
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142 '[M+CH3COO]-': 59.01385, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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143 '[M-H+CH3COOH]-': 59.01385 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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144 # same as above but different style of writing adduct |
fd5c0b39569a
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145 } |
fd5c0b39569a
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146 inv_adduct_types = {int(round(v, 0)): k for k, v in adduct_types.iteritems()} |
fd5c0b39569a
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147 |
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148 |
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149 # function to extract the meta data using the regular expressions |
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150 def parse_meta(meta_regex, meta_info=None): |
fd5c0b39569a
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151 if meta_info is None: |
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152 meta_info = {} |
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153 for k, regexes in six.iteritems(meta_regex): |
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154 for reg in regexes: |
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155 m = re.search(reg, line, re.IGNORECASE) |
fd5c0b39569a
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156 if m: |
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157 meta_info[k] = '-'.join(m.groups()).strip() |
fd5c0b39569a
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158 return meta_info |
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159 |
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160 |
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161 ###################################################################### |
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162 # Setup parameter dictionary |
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163 ###################################################################### |
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164 def init_paramd(args): |
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165 paramd = defaultdict() |
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166 |
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167 paramd["MetFragDatabaseType"] = args.MetFragDatabaseType |
fd5c0b39569a
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168 |
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169 if args.MetFragDatabaseType == "LocalCSV": |
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170 paramd["LocalDatabasePath"] = args.LocalDatabasePath |
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171 elif args.MetFragDatabaseType == "MetChem": |
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172 paramd["LocalMetChemDatabase"] = \ |
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173 config.get('MetChem', 'LocalMetChemDatabase') |
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174 paramd["LocalMetChemDatabasePortNumber"] = \ |
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175 config.get('MetChem', 'LocalMetChemDatabasePortNumber') |
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176 paramd["LocalMetChemDatabaseServerIp"] = \ |
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177 args.LocalMetChemDatabaseServerIp |
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178 paramd["LocalMetChemDatabaseUser"] = \ |
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179 config.get('MetChem', 'LocalMetChemDatabaseUser') |
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180 paramd["LocalMetChemDatabasePassword"] = \ |
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181 config.get('MetChem', 'LocalMetChemDatabasePassword') |
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182 |
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183 paramd["FragmentPeakMatchAbsoluteMassDeviation"] = \ |
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184 args.FragmentPeakMatchAbsoluteMassDeviation |
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185 paramd["FragmentPeakMatchRelativeMassDeviation"] = \ |
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186 args.FragmentPeakMatchRelativeMassDeviation |
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187 paramd["DatabaseSearchRelativeMassDeviation"] = \ |
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188 args.DatabaseSearchRelativeMassDeviation |
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189 paramd["SampleName"] = '' |
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190 paramd["ResultsPath"] = os.path.join(wd) |
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191 |
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192 if args.polarity == "pos": |
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193 paramd["IsPositiveIonMode"] = True |
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194 paramd["PrecursorIonModeDefault"] = "1" |
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195 paramd["PrecursorIonMode"] = "1" |
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196 paramd["nm_mass_diff_default"] = 1.007276 |
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197 else: |
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198 paramd["IsPositiveIonMode"] = False |
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199 paramd["PrecursorIonModeDefault"] = "-1" |
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200 paramd["PrecursorIonMode"] = "-1" |
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201 paramd["nm_mass_diff_default"] = -1.007276 |
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202 |
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203 paramd["MetFragCandidateWriter"] = "CSV" |
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204 paramd["NumberThreads"] = args.NumberThreads |
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205 |
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206 if args.ScoreSuspectLists: |
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207 paramd["ScoreSuspectLists"] = args.ScoreSuspectLists |
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208 |
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209 paramd["MetFragScoreTypes"] = args.MetFragScoreTypes |
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210 paramd["MetFragScoreWeights"] = args.MetFragScoreWeights |
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211 |
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212 dct_filter = defaultdict() |
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213 filterh = [] |
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214 |
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215 if args.UnconnectedCompoundFilter: |
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216 filterh.append('UnconnectedCompoundFilter') |
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217 |
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218 if args.IsotopeFilter: |
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219 filterh.append('IsotopeFilter') |
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220 |
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221 if args.FilterMinimumElements: |
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222 filterh.append('MinimumElementsFilter') |
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223 dct_filter['FilterMinimumElements'] = args.FilterMinimumElements |
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224 |
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225 if args.FilterMaximumElements: |
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226 filterh.append('MaximumElementsFilter') |
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227 dct_filter['FilterMaximumElements'] = args.FilterMaximumElements |
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228 |
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229 if args.FilterSmartsInclusionList: |
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230 filterh.append('SmartsSubstructureInclusionFilter') |
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231 dct_filter[ |
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232 'FilterSmartsInclusionList'] = args.FilterSmartsInclusionList |
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233 |
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234 if args.FilterSmartsExclusionList: |
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235 filterh.append('SmartsSubstructureExclusionFilter') |
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236 dct_filter[ |
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237 'FilterSmartsExclusionList'] = args.FilterSmartsExclusionList |
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238 |
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239 # My understanding is that both 'ElementInclusionExclusiveFilter' |
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240 # and 'ElementExclusionFilter' use 'FilterIncludedElements' |
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241 if args.FilterIncludedExclusiveElements: |
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242 filterh.append('ElementInclusionExclusiveFilter') |
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243 dct_filter[ |
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244 'FilterIncludedElements'] = args.FilterIncludedExclusiveElements |
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245 |
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246 if args.FilterIncludedElements: |
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247 filterh.append('ElementInclusionFilter') |
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248 dct_filter['FilterIncludedElements'] = args.FilterIncludedElements |
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249 |
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250 if args.FilterExcludedElements: |
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251 filterh.append('ElementExclusionFilter') |
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252 dct_filter['FilterExcludedElements'] = args.FilterExcludedElements |
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253 |
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254 if filterh: |
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255 fcmds = ','.join(filterh) + ' ' |
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256 for k, v in six.iteritems(dct_filter): |
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257 fcmds += "{0}={1} ".format(str(k), str(v)) |
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258 |
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259 paramd["MetFragPreProcessingCandidateFilter"] = fcmds |
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260 |
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261 return paramd |
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262 |
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263 |
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264 ###################################################################### |
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265 # Function to run metfrag when all metainfo and peaks have been parsed |
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266 ###################################################################### |
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267 def run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types): |
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268 # Get sample details (if possible to extract) e.g. if created as part of |
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269 # the msPurity pipeline) choose between getting additional details to add |
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270 # as columns as either all meta data from msp, just details from the |
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271 # record name (i.e. when using msPurity and we have the columns coded into |
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272 # the name) or just the spectra index (spectrac)]. |
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273 # Returns the parameters used and the command line call |
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274 |
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275 paramd = init_paramd(args) |
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276 if args.meta_select_col == 'name': |
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277 # have additional column of just the name |
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278 paramd['additional_details'] = {'name': meta_info['name']} |
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279 elif args.meta_select_col == 'name_split': |
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280 # have additional columns split by "|" and |
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281 # then on ":" e.g. MZ:100.2 | RT:20 | xcms_grp_id:1 |
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282 paramd['additional_details'] = { |
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283 sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in |
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284 meta_info['name'].split("|")} |
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285 elif args.meta_select_col == 'all': |
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286 # have additional columns based on all the meta information |
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287 # extracted from the MSP |
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288 paramd['additional_details'] = meta_info |
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289 else: |
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290 # Just have and index of the spectra in the MSP file |
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291 paramd['additional_details'] = {'spectra_idx': spectrac} |
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292 |
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293 paramd["SampleName"] = "{}_metfrag_result".format(spectrac) |
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294 |
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295 # =============== Output peaks to txt file ============================== |
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296 paramd["PeakListPath"] = os.path.join(wd, |
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297 "{}_tmpspec.txt".format(spectrac)) |
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298 |
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299 # write spec file |
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300 with open(paramd["PeakListPath"], 'w') as outfile: |
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301 for p in peaklist: |
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302 outfile.write(p[0] + "\t" + p[1] + "\n") |
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303 |
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304 # =============== Update param based on MSP metadata ====================== |
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305 # Replace param details with details from MSP if required |
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306 if 'precursor_type' in meta_info and \ |
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307 meta_info['precursor_type'] in adduct_types: |
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308 adduct = meta_info['precursor_type'] |
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309 nm = float(meta_info['precursor_mz']) - adduct_types[ |
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310 meta_info['precursor_type']] |
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311 paramd["PrecursorIonMode"] = \ |
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312 int(round(adduct_types[meta_info['precursor_type']], 0)) |
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313 elif not args.skip_invalid_adducts: |
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314 adduct = inv_adduct_types[int(paramd['PrecursorIonModeDefault'])] |
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315 paramd["PrecursorIonMode"] = paramd['PrecursorIonModeDefault'] |
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316 nm = float(meta_info['precursor_mz']) - paramd['nm_mass_diff_default'] |
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317 else: |
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318 print('Skipping {}'.format(paramd["SampleName"])) |
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319 return '', '' |
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320 |
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321 paramd['additional_details']['adduct'] = adduct |
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322 paramd["NeutralPrecursorMass"] = nm |
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323 |
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324 # ============== Create CLI cmd for metfrag =============================== |
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325 cmd = "metfrag" |
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326 for k, v in six.iteritems(paramd): |
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327 if k not in ['PrecursorIonModeDefault', 'nm_mass_diff_default', |
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328 'additional_details']: |
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329 cmd += " {}={}".format(str(k), str(v)) |
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330 |
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331 # ============== Run metfrag ============================================== |
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332 # print(cmd) |
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333 # Filter before process with a minimum number of MS/MS peaks |
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334 if plinesread >= float(args.minMSMSpeaks): |
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335 |
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336 if int(args.cores_top_level) == 1: |
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337 os.system(cmd) |
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338 |
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339 return paramd, cmd |
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340 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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341 |
fd5c0b39569a
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342 def work(cmds): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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343 return [os.system(cmd) for cmd in cmds] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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344 |
fd5c0b39569a
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computational-metabolomics
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345 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
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346 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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347 # Parse MSP file and run metfrag CLI |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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348 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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349 # keep list of commands if performing in CLI in parallel |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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350 cmds = [] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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351 # keep a dictionary of all params |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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352 paramds = {} |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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353 # keep count of spectra (for uid) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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354 spectrac = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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355 # this dictionary will store the meta data results form the MSp file |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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356 meta_info = {} |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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357 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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358 with open(args.input_pth, "r") as infile: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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359 # number of lines for the peaks |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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360 pnumlines = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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361 # number of lines read for the peaks |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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362 plinesread = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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363 for line in infile: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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364 line = line.strip() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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365 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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366 if pnumlines == 0: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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367 # ============== Extract metadata from MSP ======================== |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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368 meta_info = parse_meta(meta_regex, meta_info) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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369 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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370 if ('massbank' in meta_info and 'cols' in meta_info) or ( |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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371 'msp' in meta_info and 'num_peaks' in meta_info): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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372 pnumlines = int(meta_info['num_peaks']) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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373 plinesread = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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374 peaklist = [] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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375 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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376 elif plinesread < pnumlines: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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377 # ============== Extract peaks from MSP ========================== |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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378 # .split() will split on any empty space (i.e. tab and space) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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379 line = tuple(line.split()) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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380 # Keep only m/z and intensity, not relative intensity |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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381 save_line = tuple(line[0].split() + line[1].split()) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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382 plinesread += 1 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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383 peaklist.append(save_line) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
384 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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385 elif plinesread and plinesread == pnumlines: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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386 # ======= Get sample name and additional details for output ======= |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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387 spectrac += 1 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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388 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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389 adduct_types) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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|
390 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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391 if paramd: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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392 paramds[paramd["SampleName"]] = paramd |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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393 cmds.append(cmd) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
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|
394 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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395 meta_info = {} |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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396 pnumlines = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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397 plinesread = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
398 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
399 # end of file. Check if there is a MSP spectra to run metfrag on still |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
400 if plinesread and plinesread == pnumlines: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
401 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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402 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac + 1, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
403 adduct_types) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
404 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
405 if paramd: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
406 paramds[paramd["SampleName"]] = paramd |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
407 cmds.append(cmd) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
408 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
409 # Perform multiprocessing on command line call level |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
410 if int(args.cores_top_level) > 1: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
411 cmds_chunks = [cmds[x:x + int(args.chunks)] for x in |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
412 list(range(0, len(cmds), int(args.chunks)))] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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413 pool = multiprocessing.Pool(processes=int(args.cores_top_level)) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
414 pool.map(work, cmds_chunks) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
415 pool.close() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
416 pool.join() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
417 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
418 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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419 # Concatenate and filter the output |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
420 ###################################################################### |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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421 # outputs might have different headers. Need to get a list of all the |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
422 # headers before we start merging the files |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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423 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
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|
424 # "*_metfrag_result.csv"))] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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425 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv")) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
426 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
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|
427 if len(outfiles) == 0: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
428 print('No results') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
429 sys.exit() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
430 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
431 headers = [] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
432 c = 0 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
433 for fn in outfiles: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
434 with open(fn, 'r') as infile: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
435 reader = csv.reader(infile) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
436 if sys.version_info >= (3, 0): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
437 headers.extend(next(reader)) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
438 else: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
439 headers.extend(reader.next()) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
440 # check if file has any data rows |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
441 for i, row in enumerate(reader): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
442 c += 1 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
443 if i == 1: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
444 break |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
445 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
446 # if no data rows (e.g. matches) then do not save an |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
447 # output and leave the program |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
448 if c == 0: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
449 print('No results') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
450 sys.exit() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
451 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
452 additional_detail_headers = ['sample_name'] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
453 for k, paramd in six.iteritems(paramds): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
454 additional_detail_headers = list(set( |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
455 additional_detail_headers + list(paramd['additional_details'].keys()))) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
456 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
457 # add inchikey if not already present (missing in metchem output) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
458 if 'InChIKey' not in headers: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
459 headers.append('InChIKey') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
460 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
461 headers = additional_detail_headers + sorted(list(set(headers))) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
462 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
463 # Sort files nicely |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
464 outfiles.sort( |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
465 key=lambda s: int(re.match(r'^.*/(\d+)_metfrag_result.csv', s).group(1))) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
466 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
467 print(outfiles) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
468 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
469 # merge outputs |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
470 with open(args.result_pth, 'a') as merged_outfile: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
471 dwriter = csv.DictWriter(merged_outfile, fieldnames=headers, |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
472 delimiter='\t', quotechar='"') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
473 dwriter.writeheader() |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
474 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
475 for fn in outfiles: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
476 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
477 with open(fn) as infile: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
478 reader = csv.DictReader(infile, delimiter=',', quotechar='"') |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
479 for line in reader: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
480 bewrite = True |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
481 for key, value in line.items(): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
482 # Filter when no MS/MS peak matched |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
483 if key == "ExplPeaks": |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
484 if float(args.pctexplpeak_thrshld) > 0 and \ |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
485 "NA" in value: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
486 bewrite = False |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
487 # Filter with a score threshold |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
488 elif key == "Score": |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
489 if float(value) <= float(args.score_thrshld): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
490 bewrite = False |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
491 elif key == "NoExplPeaks": |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
492 nbfindpeak = float(value) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
493 elif key == "NumberPeaksUsed": |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
494 totpeaks = float(value) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
495 # Filter with a relative number of peak matched |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
496 try: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
497 pctexplpeak = nbfindpeak / totpeaks * 100 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
498 except ZeroDivisionError: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
499 bewrite = False |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
500 else: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
501 if pctexplpeak < float(args.pctexplpeak_thrshld): |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
502 bewrite = False |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
503 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
504 # Write the line if it pass all filters |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
505 if bewrite: |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
506 bfn = os.path.basename(fn) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
507 bfn = bfn.replace(".csv", "") |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
508 line['sample_name'] = paramds[bfn]['SampleName'] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
509 ad = paramds[bfn]['additional_details'] |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
510 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
511 if args.MetFragDatabaseType == "MetChem": |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
512 # for some reason the metchem database option does |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
513 # not report the full inchikey (at least in the Bham |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
514 # setup. This ensures we always get the fully inchikey |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
515 line['InChIKey'] = '{}-{}-{}'.format(line['InChIKey1'], |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
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516 line['InChIKey2'], |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
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517 line['InChIKey3']) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
|
518 |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
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519 line.update(ad) |
fd5c0b39569a
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit e20ce56f23d9fe30df64542ece2295d654ca142d"
computational-metabolomics
parents:
diff
changeset
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520 dwriter.writerow(line) |