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annotate mqwrapper.py @ 2:666f3453a99d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 2131f017e9303599ed672797ffd6e9b00ab1245d
author galaxyp
date Wed, 07 Aug 2019 10:50:06 -0400
parents 8bac3cc5c5de
children 175e062b6a17
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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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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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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 'exp_design', '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 # arguments for mqparam
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38 ## global
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39 global_flags = ('calc_peak_properties',
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40 'write_mztab',
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41 'ibaq',
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42 'ibaq_log_fit',
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43 'separate_lfq',
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44 'lfq_stabilize_large_ratios',
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45 'lfq_require_msms',
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46 'advanced_site_intensities',
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47 'match_between_runs')
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48
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49 global_simple_args = ('min_unique_pep',
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50 'num_threads',
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51 'min_peptide_len',
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52 'max_peptide_mass')
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53
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54 ## parameter group specific
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55 param_group_flags = ('lfq_skip_norm',)
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56
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57 param_group_simple_args = ('missed_cleavages',
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58 'lfq_mode',
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59 'lfq_min_edges_per_node',
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60 'lfq_avg_edges_per_node',
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61 'lfq_min_ratio_count')
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62
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63 param_group_silac_args = ('light_mods', 'medium_mods', 'heavy_mods')
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64
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65 list_args = ('fixed_mods', 'var_mods', 'proteases')
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66
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67 arguments = ['--' + el for el in (txt_output
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68 + global_simple_args
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69 + param_group_simple_args
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70 + list_args
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71 + param_group_silac_args
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72 + other_args)]
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73
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74 flags = ['--' + el for el in global_flags + param_group_flags]
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75
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76 for arg in arguments:
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77 parser.add_argument(arg)
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78 for flag in flags:
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79 parser.add_argument(flag, action="store_true")
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80
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81 args = vars(parser.parse_args())
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82
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83 # link infile datasets to names with correct extension
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84 # for maxquant to accept them
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85 files = (args['raw_files'] if args['raw_files']
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86 else args['mzxml_files']).split(',')
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87 ftype = ".thermo.raw" if args['raw_files'] else ".mzXML"
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88 filenames = args['infile_names'].split(',')
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89 fnames_with_ext = [(a if a.endswith(ftype)
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90 else os.path.splitext(a)[0] + ftype)
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91 for a in filenames]
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92
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93 for f, l in zip(files, fnames_with_ext):
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94 os.symlink(f, l)
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95
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96 # build mqpar.xml
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97 mqpar_in = os.path.join(os.getcwd(), 'mqpar.xml')
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98 subprocess.run(('maxquant', '-c', mqpar_in))
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99 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_in
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100
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101
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102 exp_design = args['exp_design'] if args['exp_design'] != 'None' else None
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103 m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design,
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104 substitution_rx=args['substitution_rx'])
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105 if m.version != args['version']:
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106 raise Exception('mqpar version is ' + m.version +
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107 '. Tool uses version {}.'.format(args['version']))
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108
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109 # modify parameters, interactive mode if no mqpar_in was specified
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110 m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], True)
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111 m.add_fasta_files(args['fasta_files'].split(','),
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112 identifier=args['identifier_parse_rule'],
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113 description=args['description_parse_rule'])
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114
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115 for e in (global_simple_args
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116 + param_group_simple_args
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117 + global_flags
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118 + param_group_flags):
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119 if args[e]:
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120 m.set_simple_param(e, args[e])
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121
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122 for e in list_args:
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123 if args[e]:
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124 m.set_list_params(e, args[e].split(','))
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125
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126 if args['light_mods'] or args['medium_mods'] or args['heavy_mods']:
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127 m.set_silac(args['light_mods'].split(',') if args['light_mods'] else None,
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128 args['medium_mods'].split(',') if args['medium_mods'] else None,
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129 args['heavy_mods'].split(',') if args['heavy_mods'] else None)
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130
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131 m.write()
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132
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133 # build and run MaxQuant command
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134 cmd = ['maxquant', mqpar_out]
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135
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136 subprocess.run(cmd, check=True, cwd='./')
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137
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138 # copy results to galaxy database
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139 for el in txt_output:
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140 destination = args[el]
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141 source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el))
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142 if destination != 'None' and os.path.isfile(source):
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143 shutil.copy(source, destination)
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144
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145 if args['mzTab'] != 'None':
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146 source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab")
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147 if os.path.isfile(source):
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148 shutil.copy(source, args['mzTab'])