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annotate mqparam.py @ 1:8bac3cc5c5de 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 05:01:05 -0400
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8bac3cc5c5de 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 Create a project-specific MaxQuant parameter file.
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3
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4 TODO: check validity of parsed experimental design template
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5 add support for parameter groups
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6 add reporter ion MS2
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7 add label free quantification
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8 don't hardcode parse rules for fasta files
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9
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10 Author: Damian Glaetzer <d.glaetzer@mailbox.org>
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11 """
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12
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13 import ntpath
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14 import os
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15 import re
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16 import xml.etree.ElementTree as ET
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17 from itertools import zip_longest
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18 from xml.dom import minidom
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19
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21 class MQParam:
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22 """Represents a mqpar.xml and provides methods to modify
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23 some of its parameters.
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24 """
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25
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26 fasta_template = """<FastaFileInfo>
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27 <fastaFilePath></fastaFilePath>
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28 <identifierParseRule></identifierParseRule>
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29 <descriptionParseRule></descriptionParseRule>
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30 <taxonomyParseRule></taxonomyParseRule>
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31 <variationParseRule></variationParseRule>
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32 <modificationParseRule></modificationParseRule>
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33 <taxonomyId></taxonomyId>
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34 </FastaFileInfo>"""
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35
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36 def __init__(self, mqpar_out, mqpar_in, exp_design,
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37 substitution_rx=r'[^\s\S]'): # no sub by default
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38 """Initialize MQParam class. mqpar_in can either be a template
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39 or a already suitable mqpar file.
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40 >>> t = MQParam("test", './test-data/template.xml', None)
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41 >>> t.root.tag
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42 'MaxQuantParams'
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43 >>> (t.root.find('maxQuantVersion')).text
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44 '1.6.3.4'
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45 """
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46
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47 self.orig_mqpar = mqpar_in
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48 self.exp_design = exp_design
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49 self.mqpar_out = mqpar_out
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50 self.root = ET.parse(mqpar_in).getroot()
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51 self.version = self.root.find('maxQuantVersion').text
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52 # regex for substitution of certain file name characters
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53 self.substitution_rx = substitution_rx
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54
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55 @staticmethod
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56 def _add_child(el, name, text, attrib=None):
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57 """Add a child element to an element.
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58
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59 >>> t = MQParam("test", './test-data/template.xml', None)
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60 >>> MQParam._add_child(t.root, "test", "test")
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61 >>> t.root.find('test').text == "test"
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62 True
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63 """
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64
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65 child = ET.SubElement(el, name, attrib=attrib if attrib else {})
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66 child.text = str(text)
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67
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68 def _make_exp_design(self, infiles):
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69 """Create a dict representing an experimental design from
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70 an experimental design template and a list of input files.
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71 If the experimental design template is None, create a default
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72 design with one experiment for each input file, no fractions and
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73 parameter group 0 for all files.
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74 >>> t2 = MQParam("test", './test-data/template.xml', \
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75 './test-data/two/exp_design_template.txt')
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76 >>> design = t2._make_exp_design(['./test-data/BSA_min_21.mzXML', \
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77 './test-data/BSA_min_22.mzXML'])
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78 >>> design['Name']
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79 ['./test-data/BSA_min_21.mzXML', './test-data/BSA_min_22.mzXML']
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80 >>> design['Fraction']
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81 ['1', '2']
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82 """
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83 design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment")}
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84 if not self.exp_design:
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85 design["Name"] = infiles
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86 design["Fraction"] = ('32767',) * len(infiles)
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87 design["Experiment"] = [os.path.split(f)[1] for f in infiles]
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88 design["PTM"] = ('False',) * len(infiles)
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89 else:
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90 with open(self.exp_design) as design_file:
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91 index_line = design_file.readline().strip()
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92 index = []
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93 for i in index_line.split('\t'):
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94 if i in design:
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95 index.append(i)
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96 else:
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97 raise Exception("Invalid comlumn index in experimental"
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98 + " design template: {}".format(i))
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99 for line in design_file:
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100 row = line.strip().split('\t')
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101 for e, i in zip_longest(row, index):
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102 design[i].append(e)
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103
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104 # map infiles to names in exp. design template
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105 names = []
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106 names_to_paths = {}
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107 # strip path and extension
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108 for f in infiles:
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109 b = os.path.basename(f)
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110 basename = b[:-6] if b.endswith('.mzXML') else b[:-11]
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111 names_to_paths[basename] = f
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112 for name in design['Name']:
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113 # same substitution as in maxquant.xml,
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114 # when passing the element identifiers
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115 fname = re.sub(self.substitution_rx, '_', name)
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116 names.append(names_to_paths[fname] if fname in names_to_paths
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117 else None)
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118 # replace orig. file names with matching links to galaxy datasets
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119 design['Name'] = names
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120
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121 return design
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122
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123 def add_infiles(self, infiles, interactive):
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124 """Add a list of raw/mzxml files to the mqpar.xml.
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125 If experimental design template was specified,
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126 modify other parameters accordingly.
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127 The files must be specified as absolute paths
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128 for maxquant to find them.
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129 >>> t1 = MQParam("test", './test-data/template.xml', None)
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130 >>> t1.add_infiles(('test1', ), True)
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131 >>> t1.root.find("filePaths")[0].text
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132 'test1'
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133 >>> t1.root.find("fractions")[0].text
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134 '32767'
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135 >>> len(t1.root.find("fractions"))
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136 1
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137 >>> t2 = MQParam("test", './test-data/template.xml', \
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138 './test-data/exp_design_test.txt')
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139 >>> t2.add_infiles(('test-data/QEplus021874.thermo.raw', \
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140 'test-data/QEplus021876.thermo.raw'), True)
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141 >>> len(t2.root.find("filePaths"))
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142 2
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143 >>> t2.root.find("filePaths")[1].text
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144 'test-data/QEplus021876.thermo.raw'
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145 >>> t2.root.find("experiments")[1].text
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146 '2'
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147 >>> t2.root.find("fractions")[0].text
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148 '3'
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149 """
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150
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151 # Create experimental design for interactive mode.
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152 # In non-interactive mode only filepaths are modified, but
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153 # their order from the original mqpar must be kept.
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154 if interactive:
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155 index = range(len(infiles))
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156 nodenames = ('filePaths', 'experiments', 'fractions',
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157 'ptms', 'paramGroupIndices', 'referenceChannel')
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158 design = self._make_exp_design(infiles)
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159 else:
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160 index = [-1] * len(infiles)
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161 # kind of a BUG: fails if filename starts with '.'
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162 infilenames = [os.path.basename(f).split('.')[0] for f in infiles]
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163 i = 0
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164 for child in self.root.find('filePaths'):
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165 # either windows or posix path
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166 win = ntpath.basename(child.text)
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167 posix = os.path.basename(child.text)
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168 basename = win if len(win) < len(posix) else posix
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169 basename_with_sub = re.sub(self.substitution_rx, '_',
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170 basename.split('.')[0])
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171 # match infiles to their names in mqpar.xml,
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172 # ignore files missing in mqpar.xml
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173 if basename_with_sub in infilenames:
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174 index[i] = infilenames.index(basename_with_sub)
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175 i += 1
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176 else:
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177 raise ValueError("no matching infile found for "
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178 + child.text)
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179
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180 nodenames = ('filePaths', )
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181 design = {'Name': infiles}
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182
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183 # Get parent nodes from document
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184 nodes = dict()
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185 for nodename in nodenames:
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186 node = self.root.find(nodename)
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187 if node is None:
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188 raise ValueError('Element {} not found in parameter file'
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189 .format(nodename))
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190 nodes[nodename] = node
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191 node.clear()
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192 node.tag = nodename
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193
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194 # Append sub-elements to nodes (one per file)
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195 for i in index:
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196 if i > -1 and design['Name'][i]:
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197 MQParam._add_child(nodes['filePaths'], 'string',
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198 design['Name'][i])
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199 if interactive:
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200 MQParam._add_child(nodes['experiments'], 'string',
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201 design['Experiment'][i])
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202 MQParam._add_child(nodes['fractions'], 'short',
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203 design['Fraction'][i])
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204 MQParam._add_child(nodes['ptms'], 'boolean',
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205 design['PTM'][i])
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206 MQParam._add_child(nodes['paramGroupIndices'], 'int', 0)
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207 MQParam._add_child(nodes['referenceChannel'], 'string', '')
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208
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209 def add_fasta_files(self, files,
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210 identifier=r'>([^\s]*)',
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211 description=r'>(.*)'):
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212 """Add fasta file groups.
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213 >>> t = MQParam('test', './test-data/template.xml', None)
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214 >>> t.add_fasta_files(('test1', 'test2'))
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215 >>> len(t.root.find('fastaFiles'))
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216 2
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217 >>> t.root.find('fastaFiles')[0].find("fastaFilePath").text
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218 'test1'
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219 """
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220 fasta_node = self.root.find("fastaFiles")
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221 fasta_node.clear()
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222 fasta_node.tag = "fastaFiles"
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223
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224 for index in range(len(files)):
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225 filepath = '<fastaFilePath>' + files[index]
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226 fasta = self.fasta_template.replace('<fastaFilePath>', filepath)
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227 fasta = fasta.replace('<identifierParseRule>',
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228 '<identifierParseRule>' + identifier)
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229 fasta = fasta.replace('<descriptionParseRule>',
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230 '<descriptionParseRule>' + description)
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231 ff_node = self.root.find('.fastaFiles')
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232 fastaentry = ET.fromstring(fasta)
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233 ff_node.append(fastaentry)
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234
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235 def set_simple_param(self, key, value):
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236 """Set a simple parameter.
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237 >>> t = MQParam(None, './test-data/template.xml', None)
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238 >>> t.set_simple_param('min_unique_pep', 4)
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239 >>> t.root.find('.minUniquePeptides').text
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240 '4'
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241 """
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242 # map simple params to their node in the xml tree
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243 simple_params = {'missed_cleavages':
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244 '.parameterGroups/parameterGroup/maxMissedCleavages',
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245 'min_unique_pep': '.minUniquePeptides',
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246 'num_threads': 'numThreads',
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247 'calc_peak_properties': '.calcPeakProperties',
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248 'write_mztab': 'writeMzTab',
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249 'min_peptide_len': 'minPepLen',
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250 'max_peptide_mass': 'maxPeptideMass',
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251 'match_between_runs': 'matchBetweenRuns',
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252 'ibaq': 'ibaq', # lfq global options
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253 'ibaq_log_fit': 'ibaqLogFit',
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254 'separate_lfq': 'separateLfq',
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255 'lfq_stabilize_large_ratios':
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256 'lfqStabilizeLargeRatios',
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257 'lfq_require_msms': 'lfqRequireMsms',
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258 'advanced_site_intensities':
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259 'advancedSiteIntensities',
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260 'lfq_mode': # lfq param group options
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261 '.parameterGroups/parameterGroup/lfqMode',
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262 'lfq_skip_norm':
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263 '.parameterGroups/parameterGroup/lfqSkipNorm',
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264 'lfq_min_edges_per_node':
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265 '.parameterGroups/parameterGroup/lfqMinEdgesPerNode',
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266 'lfq_avg_edges_per_node':
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267 '.parameterGroups/parameterGroup/lfqAvEdgesPerNode',
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268 'lfq_min_ratio_count':
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269 '.parameterGroups/parameterGroup/lfqMinRatioCount'}
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270
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271 if key in simple_params:
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272 node = self.root.find(simple_params[key])
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273 if node is None:
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274 raise ValueError('Element {} not found in parameter file'
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275 .format(simple_params[key]))
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276 node.text = str(value)
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277 else:
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278 raise ValueError("Parameter not found.")
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279
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280 def set_silac(self, light_mods, medium_mods, heavy_mods):
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281 """Set label modifications.
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282 >>> t1 = MQParam('test', './test-data/template.xml', None)
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283 >>> t1.set_silac(None, ('test1', 'test2'), None)
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284 >>> t1.root.find('.parameterGroups/parameterGroup/maxLabeledAa').text
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285 '2'
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286 >>> t1.root.find('.parameterGroups/parameterGroup/multiplicity').text
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287 '3'
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288 >>> t1.root.find('.parameterGroups/parameterGroup/labelMods')[1].text
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289 'test1;test2'
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290 >>> t1.root.find('.parameterGroups/parameterGroup/labelMods')[2].text
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291 ''
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292 """
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293 multiplicity = 3 if medium_mods else 2 if heavy_mods else 1
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294 max_label = str(max(len(light_mods) if light_mods else 0,
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295 len(medium_mods) if medium_mods else 0,
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296 len(heavy_mods) if heavy_mods else 0))
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297 multiplicity_node = self.root.find('.parameterGroups/parameterGroup/'
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298 + 'multiplicity')
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299 multiplicity_node.text = str(multiplicity)
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300 max_label_node = self.root.find('.parameterGroups/parameterGroup/'
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301 + 'maxLabeledAa')
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302 max_label_node.text = max_label
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303
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304 node = self.root.find('.parameterGroups/parameterGroup/labelMods')
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305 node[0].text = ';'.join(light_mods) if light_mods else ''
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306 if multiplicity == 3:
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307 MQParam._add_child(node, name='string', text=';'.join(medium_mods))
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308 if multiplicity > 1:
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309 MQParam._add_child(node, name='string',
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310 text=';'.join(heavy_mods) if heavy_mods else '')
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311
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312 def set_list_params(self, key, vals):
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313 """Set a list parameter.
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314 >>> t = MQParam(None, './test-data/template.xml', None)
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315 >>> t.set_list_params('proteases', ('test 1', 'test 2'))
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316 >>> len(t.root.find('.parameterGroups/parameterGroup/enzymes'))
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317 2
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318 >>> t.set_list_params('var_mods', ('Oxidation (M)', ))
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319 >>> var_mods = '.parameterGroups/parameterGroup/variableModifications'
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320 >>> t.root.find(var_mods)[0].text
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321 'Oxidation (M)'
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322 """
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323
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324 params = {'var_mods':
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325 '.parameterGroups/parameterGroup/variableModifications',
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326 'fixed_mods':
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327 '.parameterGroups/parameterGroup/fixedModifications',
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328 'proteases':
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329 '.parameterGroups/parameterGroup/enzymes'}
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330
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331 if key in params:
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332 node = self.root.find(params[key])
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333 if node is None:
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334 raise ValueError('Element {} not found in parameter file'
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335 .format(params[key]))
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336 node.clear()
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337 node.tag = params[key].split('/')[-1]
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338 for e in vals:
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339 MQParam._add_child(node, name='string', text=e)
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340 else:
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341 raise ValueError("Parameter {} not found.".format(key))
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342
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343 def write(self):
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344 rough_string = ET.tostring(self.root, 'utf-8', short_empty_elements=False)
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345 reparsed = minidom.parseString(rough_string)
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346 pretty = reparsed.toprettyxml(indent="\t")
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347 even_prettier = re.sub(r"\n\s+\n", r"\n", pretty)
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348 with open(self.mqpar_out, 'w') as f:
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349 print(even_prettier, file=f)