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annotate metfrag.py @ 8:9a3019c609d9 draft

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planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
author tomnl
date Fri, 13 Sep 2019 08:27:59 -0400
parents 0b3816a7a14b
children 5763234618d4
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1 from __future__ import absolute_import, print_function
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2 import argparse
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3 import csv
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4 import os
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5 import sys
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6 import six
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7 import re
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8 import ConfigParser
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9 import shutil
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10 import glob
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11 import tempfile
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12 import multiprocessing
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14 from subprocess import call
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15 from collections import defaultdict
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17 print(sys.version)
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--input_pth')
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21 parser.add_argument('--result_pth', default='metfrag_result.csv')
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23 parser.add_argument('--temp_dir')
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24 parser.add_argument('--polarity', default='pos')
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25 parser.add_argument('--minMSMSpeaks', default=1)
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27 parser.add_argument('--MetFragDatabaseType', default='PubChem')
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28 parser.add_argument('--LocalDatabasePath', default='')
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29 parser.add_argument('--LocalMetChemDatabaseServerIp', default='')
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31 parser.add_argument('--DatabaseSearchRelativeMassDeviation', default=5)
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32 parser.add_argument('--FragmentPeakMatchRelativeMassDeviation', default=10)
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33 parser.add_argument('--FragmentPeakMatchAbsoluteMassDeviation', default=0.001)
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34 parser.add_argument('--NumberThreads', default=1)
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35 parser.add_argument('--UnconnectedCompoundFilter', action='store_true')
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36 parser.add_argument('--IsotopeFilter', action='store_true')
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38 parser.add_argument('--FilterMinimumElements', default='')
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39 parser.add_argument('--FilterMaximumElements', default='')
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40 parser.add_argument('--FilterSmartsInclusionList', default='')
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41 parser.add_argument('--FilterSmartsExclusionList', default='')
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42 parser.add_argument('--FilterIncludedElements', default='')
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43 parser.add_argument('--FilterExcludedElements', default='')
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44 parser.add_argument('--FilterIncludedExclusiveElements', default='')
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46 parser.add_argument('--score_thrshld', default=0)
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47 parser.add_argument('--pctexplpeak_thrshld', default=0)
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48 parser.add_argument('--schema')
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49 parser.add_argument('--cores_top_level', default=1)
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50 parser.add_argument('--chunks', default=1)
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51 parser.add_argument('--meta_select_col', default='name')
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52 parser.add_argument('--skip_invalid_adducts', action='store_true')
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54 parser.add_argument('--ScoreSuspectLists', default='')
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55 parser.add_argument('--MetFragScoreTypes', default="FragmenterScore,OfflineMetFusionScore")
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56 parser.add_argument('--MetFragScoreWeights', default="1.0,1.0")
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57
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58
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59 args = parser.parse_args()
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60 print(args)
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63 config = ConfigParser.ConfigParser()
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64 config.read(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.ini'))
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66
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67 if os.stat(args.input_pth).st_size == 0:
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68 print('Input file empty')
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69 exit()
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71
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72 # Create temporary working directory
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73 if args.temp_dir:
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74 wd = args.temp_dir
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75 else:
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76 wd = tempfile.mkdtemp()
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77
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78 if os.path.exists(wd):
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79 shutil.rmtree(wd)
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80 os.makedirs(wd)
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81 else:
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82 os.makedirs(wd)
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83
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84 ######################################################################
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85 # Setup regular expressions for MSP parsing dictionary
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86 ######################################################################
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87 regex_msp = {}
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88 regex_msp['name'] = ['^Name(?:=|:)(.*)$']
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89 regex_msp['polarity'] = ['^ion.*mode(?:=|:)(.*)$', '^ionization.*mode(?:=|:)(.*)$', '^polarity(?:=|:)(.*)$']
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90 regex_msp['precursor_mz'] = ['^precursor.*m/z(?:=|:)\s*(\d*[.,]?\d*)$', '^precursor.*mz(?:=|:)\s*(\d*[.,]?\d*)$']
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91 regex_msp['precursor_type'] = ['^precursor.*type(?:=|:)(.*)$', '^adduct(?:=|:)(.*)$', '^ADDUCTIONNAME(?:=|:)(.*)$']
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92 regex_msp['num_peaks'] = ['^Num.*Peaks(?:=|:)\s*(\d*)$']
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93 regex_msp['msp'] = ['^Name(?:=|:)(.*)$'] # Flag for standard MSP format
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94
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95 regex_massbank = {}
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96 regex_massbank['name'] = ['^RECORD_TITLE:(.*)$']
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97 regex_massbank['polarity'] = ['^AC\$MASS_SPECTROMETRY:\s+ION_MODE\s+(.*)$']
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98 regex_massbank['precursor_mz'] = ['^MS\$FOCUSED_ION:\s+PRECURSOR_M/Z\s+(\d*[.,]?\d*)$']
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99 regex_massbank['precursor_type'] = ['^MS\$FOCUSED_ION:\s+PRECURSOR_TYPE\s+(.*)$']
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100 regex_massbank['num_peaks'] = ['^PK\$NUM_PEAK:\s+(\d*)']
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101 regex_massbank['cols'] = ['^PK\$PEAK:\s+(.*)']
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102 regex_massbank['massbank'] = ['^RECORD_TITLE:(.*)$'] # Flag for massbank format
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103
1
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104 if args.schema == 'msp':
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105 meta_regex = regex_msp
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106 elif args.schema == 'massbank':
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107 meta_regex = regex_massbank
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108 elif args.schema == 'auto':
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109 # If auto we just check for all the available paramter names and then determine if Massbank or MSP based on
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110 # the name parameter
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111 meta_regex = {}
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112 meta_regex.update(regex_massbank)
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113 meta_regex['name'].extend(regex_msp['name'])
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114 meta_regex['polarity'].extend(regex_msp['polarity'])
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115 meta_regex['precursor_mz'].extend(regex_msp['precursor_mz'])
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116 meta_regex['precursor_type'].extend(regex_msp['precursor_type'])
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117 meta_regex['num_peaks'].extend(regex_msp['num_peaks'])
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118 meta_regex['msp'] = regex_msp['msp']
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119
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120
1
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121
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122 adduct_types = {
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123 '[M+H]+': 1.007276,
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124 '[M+NH4]+': 18.034374,
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125 '[M+Na]+': 22.989218,
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126 '[M+K]+': 38.963158,
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127 '[M+CH3OH+H]+': 33.033489,
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128 '[M+ACN+H]+': 42.033823,
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129 '[M+ACN+Na]+': 64.015765,
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130 '[M+2ACN+H]+': 83.06037,
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131 '[M-H]-': -1.007276,
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132 '[M+Cl]-': 34.969402,
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133 '[M+HCOO]-': 44.99819,
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134 '[M-H+HCOOH]-': 44.99819, # same as above but different style of writing adduct
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135 '[M+CH3COO]-': 59.01385,
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136 '[M-H+CH3COOH]-': 59.01385 # same as above but different style of writing adduct
1
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137 }
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138 inv_adduct_types = {int(round(v, 0)): k for k, v in adduct_types.iteritems()}
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139
2
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140 # function to extract the meta data using the regular expressions
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141 def parse_meta(meta_regex, meta_info={}):
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142 for k, regexes in six.iteritems(meta_regex):
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143 for reg in regexes:
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144 m = re.search(reg, line, re.IGNORECASE)
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145 if m:
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146 meta_info[k] = '-'.join(m.groups()).strip()
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147 return meta_info
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148
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149
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150
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151 ######################################################################
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152 # Setup parameter dictionary
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153 ######################################################################
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154 def init_paramd(args):
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155 paramd = defaultdict()
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156
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157 paramd["MetFragDatabaseType"] = args.MetFragDatabaseType
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158
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159 if args.MetFragDatabaseType == "LocalCSV":
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160 paramd["LocalDatabasePath"] = args.LocalDatabasePath
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161 elif args.MetFragDatabaseType == "MetChem":
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162 paramd["LocalMetChemDatabase"] = config.get('MetChem', 'LocalMetChemDatabase')
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163 paramd["LocalMetChemDatabasePortNumber"] = config.get('MetChem', 'LocalMetChemDatabasePortNumber')
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164 paramd["LocalMetChemDatabaseServerIp"] = args.LocalMetChemDatabaseServerIp
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165 paramd["LocalMetChemDatabaseUser"] = config.get('MetChem', 'LocalMetChemDatabaseUser')
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166 paramd["LocalMetChemDatabasePassword"] = config.get('MetChem', 'LocalMetChemDatabasePassword')
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167
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168 paramd["FragmentPeakMatchAbsoluteMassDeviation"] = args.FragmentPeakMatchAbsoluteMassDeviation
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169 paramd["FragmentPeakMatchRelativeMassDeviation"] = args.FragmentPeakMatchRelativeMassDeviation
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170 paramd["DatabaseSearchRelativeMassDeviation"] = args.DatabaseSearchRelativeMassDeviation
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171 paramd["SampleName"] = ''
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172 paramd["ResultsPath"] = os.path.join(wd)
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173
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174 if args.polarity == "pos":
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175 paramd["IsPositiveIonMode"] = True
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176 paramd["PrecursorIonModeDefault"] = "1"
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177 paramd["PrecursorIonMode"] = "1"
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178 paramd["nm_mass_diff_default"] = 1.007276
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179 else:
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180 paramd["IsPositiveIonMode"] = False
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181 paramd["PrecursorIonModeDefault"] = "-1"
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182 paramd["PrecursorIonMode"] = "-1"
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183 paramd["nm_mass_diff_default"] = -1.007276
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184
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185 paramd["MetFragCandidateWriter"] = "CSV"
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186 paramd["NumberThreads"] = args.NumberThreads
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187
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188 if args.ScoreSuspectLists:
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189 paramd["ScoreSuspectLists"] = args.ScoreSuspectLists
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190
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191 paramd["MetFragScoreTypes"] = args.MetFragScoreTypes
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192 paramd["MetFragScoreWeights"] = args.MetFragScoreWeights
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193
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194 dct_filter = defaultdict()
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195 filterh = []
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196
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197 if args.UnconnectedCompoundFilter:
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198 filterh.append('UnconnectedCompoundFilter')
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199
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200 if args.IsotopeFilter:
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201 filterh.append('IsotopeFilter')
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202
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203 if args.FilterMinimumElements:
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204 filterh.append('MinimumElementsFilter')
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205 dct_filter['FilterMinimumElements'] = args.FilterMinimumElements
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206
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207 if args.FilterMaximumElements:
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208 filterh.append('MaximumElementsFilter')
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209 dct_filter['FilterMaximumElements'] = args.FilterMaximumElements
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210
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211 if args.FilterSmartsInclusionList:
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212 filterh.append('SmartsSubstructureInclusionFilter')
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213 dct_filter['FilterSmartsInclusionList'] = args.FilterSmartsInclusionList
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214
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215 if args.FilterSmartsExclusionList:
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216 filterh.append('SmartsSubstructureExclusionFilter')
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217 dct_filter['FilterSmartsExclusionList'] = args.FilterSmartsExclusionList
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218
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219 # My understanding is that both 'ElementInclusionExclusiveFilter' and 'ElementExclusionFilter' use
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220 # 'FilterIncludedElements'
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221 if args.FilterIncludedExclusiveElements:
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222 filterh.append('ElementInclusionExclusiveFilter')
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223 dct_filter['FilterIncludedElements'] = args.FilterIncludedExclusiveElements
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224
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225 if args.FilterIncludedElements:
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226 filterh.append('ElementInclusionFilter')
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227 dct_filter['FilterIncludedElements'] = args.FilterIncludedElements
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228
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229 if args.FilterExcludedElements:
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230 filterh.append('ElementExclusionFilter')
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231 dct_filter['FilterExcludedElements'] = args.FilterExcludedElements
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232
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233 if filterh:
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234 fcmds = ','.join(filterh) + ' '
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235 for k, v in six.iteritems(dct_filter):
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236 fcmds += "{0}={1} ".format(str(k), str(v))
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237
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238 paramd["MetFragPreProcessingCandidateFilter"] = fcmds
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239
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240 return paramd
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241
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242
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243 ######################################################################
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244 # Function to run metfrag when all metainfo and peaks have been parsed
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245 ######################################################################
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246 def run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types):
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247 # Get sample details (if possible to extract) e.g. if created as part of the msPurity pipeline)
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248 # choose between getting additional details to add as columns as either all meta data from msp, just
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249 # details from the record name (i.e. when using msPurity and we have the columns coded into the name) or
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250 # just the spectra index (spectrac)]
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251 # Returns the parameters used and the command line call
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252
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253 paramd = init_paramd(args)
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254 if args.meta_select_col == 'name':
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255 # have additional column of just the name
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256 paramd['additional_details'] = {'name': meta_info['name']}
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257 elif args.meta_select_col == 'name_split':
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258 # have additional columns split by "|" and then on ":" e.g. MZ:100.2 | RT:20 | xcms_grp_id:1
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259 paramd['additional_details'] = {sm.split(":")[0].strip(): sm.split(":")[1].strip() for sm in
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260 meta_info['name'].split("|")}
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261 elif args.meta_select_col == 'all':
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262 # have additional columns based on all the meta information extracted from the MSP
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263 paramd['additional_details'] = meta_info
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264 else:
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265 # Just have and index of the spectra in the MSP file
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266 paramd['additional_details'] = {'spectra_idx': spectrac}
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267
8
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268
2
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269 paramd["SampleName"] = "{}_metfrag_result".format(spectrac)
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270
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271 # =============== Output peaks to txt file ==============================
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272 paramd["PeakListPath"] = os.path.join(wd, "{}_tmpspec.txt".format(spectrac))
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273
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274 # write spec file
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275 with open(paramd["PeakListPath"], 'w') as outfile:
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276 for p in peaklist:
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277 outfile.write(p[0] + "\t" + p[1] + "\n")
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278
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279 # =============== Update param based on MSP metadata ======================
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280 # Replace param details with details from MSP if required
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281 if 'precursor_type' in meta_info and meta_info['precursor_type'] in adduct_types:
8
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282 adduct = meta_info['precursor_type']
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283 nm = float(meta_info['precursor_mz']) - adduct_types[meta_info['precursor_type']]
2
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284 paramd["PrecursorIonMode"] = int(round(adduct_types[meta_info['precursor_type']], 0))
4
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285 elif not args.skip_invalid_adducts:
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286 adduct = inv_adduct_types[int(paramd['PrecursorIonModeDefault'])]
4
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287 paramd["PrecursorIonMode"] = paramd['PrecursorIonModeDefault']
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288 nm = float(meta_info['precursor_mz']) - paramd['nm_mass_diff_default']
2
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289 else:
4
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290 print('Skipping {}'.format(paramd["SampleName"]))
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291 return '', ''
2
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292
8
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293 paramd['additional_details']['adduct'] = adduct
2
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294 paramd["NeutralPrecursorMass"] = nm
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295
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296 # =============== Create CLI cmd for metfrag ===============================
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297 cmd = "metfrag"
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298 for k, v in six.iteritems(paramd):
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299 if not k in ['PrecursorIonModeDefault', 'nm_mass_diff_default', 'additional_details']:
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300 cmd += " {}={}".format(str(k), str(v))
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301
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302 # =============== Run metfrag ==============================================
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303 #print(cmd)
2
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304 # Filter before process with a minimum number of MS/MS peaks
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305 if plinesread >= float(args.minMSMSpeaks):
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306
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307 if int(args.cores_top_level) == 1:
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308 os.system(cmd)
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309
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310
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311
2
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312 return paramd, cmd
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313
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314
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315 def work(cmds):
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316 return [os.system(cmd) for cmd in cmds]
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317
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318
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319
1
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320 ######################################################################
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321 # Parse MSP file and run metfrag CLI
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322 ######################################################################
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323 # keep list of commands if performing in CLI in parallel
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324 cmds = []
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325 # keep a dictionary of all params
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326 paramds = {}
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327 # keep count of spectra (for uid)
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328 spectrac = 0
2
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329 # this dictionary will store the meta data results form the MSp file
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330 meta_info = {}
1
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331
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332 with open(args.input_pth, "r") as infile:
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333 # number of lines for the peaks
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334 pnumlines = 0
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335 # number of lines read for the peaks
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336 plinesread = 0
0
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337 for line in infile:
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338 line = line.strip()
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339
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340 if pnumlines == 0:
1
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341 # =============== Extract metadata from MSP ========================
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342 meta_info = parse_meta(meta_regex, meta_info)
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343
1
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344 if ('massbank' in meta_info and 'cols' in meta_info) or ('msp' in meta_info and 'num_peaks' in meta_info):
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345
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346 pnumlines = int(meta_info['num_peaks'])
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347 plinesread = 0
0
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348 peaklist = []
1
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349
2
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350 elif plinesread < pnumlines:
1
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351 # =============== Extract peaks from MSP ==========================
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352 line = tuple(line.split()) # .split() will split on any empty space (i.e. tab and space)
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353 # Keep only m/z and intensity, not relative intensity
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354 save_line = tuple(line[0].split() + line[1].split())
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355 plinesread += 1
1
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356 peaklist.append(save_line)
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357
2
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358 elif plinesread and plinesread == pnumlines:
1
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359 # =============== Get sample name and additional details for output =======
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360 spectrac += 1
2
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361 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac, adduct_types)
1
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362
4
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363 if paramd:
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364 paramds[paramd["SampleName"]] = paramd
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365 cmds.append(cmd)
1
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366
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367 meta_info = {}
2
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368 pnumlines = 0
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369 plinesread = 0
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370
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371 # end of file. Check if there is a MSP spectra to run metfrag on still
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372 if plinesread and plinesread == pnumlines:
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373
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374 paramd, cmd = run_metfrag(meta_info, peaklist, args, wd, spectrac+1, adduct_types)
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375
4
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376 if paramd:
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377 paramds[paramd["SampleName"]] = paramd
eb581a101672 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 28da8cdf5f9cc45575b614a329da5790803e59c4
tomnl
parents: 3
diff changeset
378 cmds.append(cmd)
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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parents:
diff changeset
379
2
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
380
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
381
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
382
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
383 # Perform multiprocessing on command line call level
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
384 if int(args.cores_top_level) > 1:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
385 cmds_chunks = [cmds[x:x + int(args.chunks)] for x in list(range(0, len(cmds), int(args.chunks)))]
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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parents: 0
diff changeset
386 pool = multiprocessing.Pool(processes=int(args.cores_top_level))
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
387 pool.map(work, cmds_chunks)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
388 pool.close()
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
389 pool.join()
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
390
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
391 ######################################################################
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
392 # Concatenate and filter the output
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
393 ######################################################################
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
394 # outputs might have different headers. Need to get a list of all the headers before we start merging the files
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
395 # outfiles = [os.path.join(wd, f) for f in glob.glob(os.path.join(wd, "*_metfrag_result.csv"))]
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
396 outfiles = glob.glob(os.path.join(wd, "*_metfrag_result.csv"))
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
397
5
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
tomnl
parents: 4
diff changeset
398 if len(outfiles) == 0:
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
tomnl
parents: 4
diff changeset
399 print('No results')
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
tomnl
parents: 4
diff changeset
400 sys.exit()
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
tomnl
parents: 4
diff changeset
401
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
402 headers = []
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
403 c = 0
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
404 for fn in outfiles:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
405 with open(fn, 'r') as infile:
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
406 reader = csv.reader(infile)
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
407 if sys.version_info >= (3, 0):
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
408 headers.extend(next(reader))
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
409 else:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
410 headers.extend(reader.next())
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
411 # check if file has any data rows
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
412 for i, row in enumerate(reader):
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
413 c += 1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
414 if i == 1:
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
415 break
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
416
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
417 # if no data rows (e.g. matches) then do not save an output and leave the program
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
418 if c == 0:
5
c53ed894d736 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 826659b9105b635cf240474428122f5a269f5c88
tomnl
parents: 4
diff changeset
419 print('No results')
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
420 sys.exit()
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
421
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
422 additional_detail_headers = ['sample_name']
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
423 for k, paramd in six.iteritems(paramds):
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
424 additional_detail_headers = list(set(additional_detail_headers + list(paramd['additional_details'].keys())))
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
425
8
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
tomnl
parents: 7
diff changeset
426 # add inchikey if not already present (missing in metchem output)
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
tomnl
parents: 7
diff changeset
427 if 'InChIKey' not in headers:
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
tomnl
parents: 7
diff changeset
428 headers.append('InChIKey')
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
tomnl
parents: 7
diff changeset
429
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
430 headers = additional_detail_headers + sorted(list(set(headers)))
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
431
2
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
432
8
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
tomnl
parents: 7
diff changeset
433
2
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
434 # Sort files nicely
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
435 outfiles.sort(key = lambda s: int(re.match('^.*/(\d+)_metfrag_result.csv', s).group(1)))
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
436
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
437 print(outfiles)
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
438
d040e27b6225 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 59631850110e60900d03f642c445cc35a36414b5
tomnl
parents: 1
diff changeset
439
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
440 # merge outputs
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
441 with open(args.result_pth, 'a') as merged_outfile:
3
5ee936e570a7 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b5d5fdc81a1756000dc25d4aa672fec1ece732a
tomnl
parents: 2
diff changeset
442 dwriter = csv.DictWriter(merged_outfile, fieldnames=headers, delimiter='\t', quotechar='"')
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
443 dwriter.writeheader()
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
444
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
445 for fn in outfiles:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
446
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
447 with open(fn) as infile:
0
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
448 reader = csv.DictReader(infile, delimiter=',', quotechar='"')
75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
tomnl
parents:
diff changeset
449 for line in reader:
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
450 bewrite = True
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
451 for key, value in line.items():
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
452 # Filter when no MS/MS peak matched
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
453 if key == "ExplPeaks":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
454 if float(args.pctexplpeak_thrshld) > 0 and "NA" in value:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
455 bewrite = False
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
456 # Filter with a score threshold
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
457 elif key == "Score":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
458 if float(value) <= float(args.score_thrshld):
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
459 bewrite = False
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
460 elif key == "NoExplPeaks":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
461 nbfindpeak = float(value)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
462 elif key == "NumberPeaksUsed":
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
463 totpeaks = float(value)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
464 # Filter with a relative number of peak matched
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
465 try:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
466 pctexplpeak = nbfindpeak / totpeaks * 100
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
467 except ZeroDivisionError:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
468 bewrite = False
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
469 else:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
tomnl
parents: 0
diff changeset
470 if pctexplpeak < float(args.pctexplpeak_thrshld):
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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471 bewrite = False
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75c805123b45 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b5f4005c77b275b9b1b4349b08476afc783a8e14
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472
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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473 # Write the line if it pass all filters
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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474 if bewrite:
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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475 bfn = os.path.basename(fn)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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476 bfn = bfn.replace(".csv", "")
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9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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477 line['sample_name'] = paramds[bfn]['SampleName']
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c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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478 ad = paramds[bfn]['additional_details']
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9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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479
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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480 if args.MetFragDatabaseType == "MetChem":
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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481 # for some reason the metchem database option does not report the full inchikey (at least
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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482 # in the Bham setup. This ensures we always get the fully inchikey
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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483 line['InChIKey'] = '{}-{}-{}'.format(line['InChIKey1'], line['InChIKey2'], line['InChIKey3'])
9a3019c609d9 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit febaaca439248736775db9ad0a857e30463d10aa
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484
1
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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485 line.update(ad)
c1b168770b68 planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 5b384bd55e5bb4b0dc1daebd2ef5d3ee0e379b2e-dirty
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486 dwriter.writerow(line)