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annotate mqwrapper.py @ 0:256cc0e17454 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
author galaxyp
date Sat, 20 Jul 2019 04:53:23 -0400
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1 """
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2 Run MaxQuant on a modified mqpar.xml.
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3 Use maxquant conda package.
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4 TODO: add support for parameter groups
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5
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6 Authors: Damian Glaetzer <d.glaetzer@mailbox.org>
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7
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8 based on the maxquant galaxy tool by John Chilton:
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9 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant
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10 """
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11
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12 import argparse
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13 import os
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14 import shutil
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15 import subprocess
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17 import mqparam
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19 # build parser
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20 parser = argparse.ArgumentParser()
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22 # input, special outputs and others
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23 other_args = ('raw_files', 'mzxml_files', 'fasta_files',
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24 'description_parse_rule', 'identifier_parse_rule',
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25 'mqpar_in', 'output_all',
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26 'mqpar_out', 'infile_names', 'mzTab',
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27 'version', 'substitution_rx')
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28
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29 # txt result files
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30 txt_output = ('evidence', 'msms', 'parameters',
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31 'peptides', 'proteinGroups', 'allPeptides',
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32 'libraryMatch', 'matchedFeatures',
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33 'modificationSpecificPeptides', 'ms3Scans',
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34 'msmsScans', 'mzRange', 'peptideSection',
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35 'summary')
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36
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37 global_simple_args = ('num_threads',)
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38
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39 arguments = ['--' + el for el in (txt_output
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40 + other_args
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41 + global_simple_args)]
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42
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43 for arg in arguments:
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44 parser.add_argument(arg)
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45
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46 args = vars(parser.parse_args())
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47
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48 # link infile datasets to names with correct extension
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49 # for maxquant to accept them
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50 files = (args['raw_files'] if args['raw_files']
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51 else args['mzxml_files']).split(',')
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52 ftype = ".thermo.raw" if args['raw_files'] else ".mzXML"
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53 filenames = args['infile_names'].split(',')
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54 fnames_with_ext = [(a if a.endswith(ftype)
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55 else os.path.splitext(a)[0] + ftype)
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56 for a in filenames]
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57
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58 for f, l in zip(files, fnames_with_ext):
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59 os.link(f, l)
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61 # build mqpar.xml
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62 mqpar_temp = os.path.join(os.getcwd(), 'mqpar.xml')
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63 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_temp
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64 mqpar_in = args['mqpar_in']
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65
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66 exp_design = None
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67 m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design,
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68 substitution_rx=args['substitution_rx'])
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69 if m.version != args['version']:
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70 raise Exception('mqpar version is ' + m.version +
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71 '. Tool uses version {}.'.format(args['version']))
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72
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73 # modify parameters, interactive mode if no mqpar_in was specified
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74 m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], False)
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75 m.add_fasta_files(args['fasta_files'].split(','),
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76 identifier=args['identifier_parse_rule'],
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77 description=args['description_parse_rule'])
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78
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79 m.write()
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80
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81 # build and run MaxQuant command
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82 cmd = ['maxquant', mqpar_out]
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83
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84 subprocess.run(cmd, check=True, cwd='./')
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85
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86 # copy results to galaxy database
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87 for el in txt_output:
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88 destination = args[el]
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89 source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el))
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90 if destination != 'None' and os.path.isfile(source):
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91 shutil.copy(source, destination)
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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92
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93 if args['mzTab'] != 'None':
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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94 source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab")
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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95 if os.path.isfile(source):
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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96 shutil.copy(source, args['mzTab'])
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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97
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98 if args['output_all'] != 'None':
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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99 subprocess.run(('tar', '-zcf', args['output_all'], './combined/txt/'))