Mercurial > repos > galaxyp > maxquant_mqpar

annotate mqparam.py @ 3:2d67fb758956 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
author galaxyp
date Sat, 11 Apr 2020 11:50:09 -0400
parents 256cc0e17454
children 9cb7dcc07dae
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1 """
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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2 Create a project-specific MaxQuant parameter file.
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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3 """
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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4
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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5 import copy
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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6 import ntpath
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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7 import os
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8 import re
3
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9 import yaml
0
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10 import xml.etree.ElementTree as ET
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11 from itertools import zip_longest
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12 from xml.dom import minidom
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13
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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14
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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15 def et_add_child(el, name, text, attrib=None):
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16 "Add a child element to an xml.etree.ElementTree.Element"
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17 child = ET.SubElement(el, name, attrib=attrib if attrib else {})
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18 child.text = str(text)
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19 return child
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22 class ParamGroup:
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23 """Represents one parameter Group
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24 """
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26 def __init__(self, root):
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27 """Initialize with its xml.etree.ElementTree root Element.
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28 """
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29 self._root = copy.deepcopy(root)
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30
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31 def set_list_param(self, key, vals):
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32 """Set a list parameter.
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33 """
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34 node = self._root.find(key)
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35 if node is None:
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36 raise ValueError('Element {} not found in parameter file'
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37 .format(key))
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38 node.clear()
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39 node.tag = key
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40 for e in vals:
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41 et_add_child(node, name='string', text=e)
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42
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43 def set_simple_param(self, key, value):
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44 """Set a simple parameter.
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45 """
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46 node = self._root.find(key)
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47 if node is None:
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48 raise ValueError('Element {} not found in parameter file'
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49 .format(key))
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50 node.text = str(value)
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51
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52 def set_silac(self, light_labels, medium_labels, heavy_labels):
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53 """Set label modifications.
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54 """
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55 if medium_labels and not (heavy_labels or light_labels): # medium omly with heavy and light
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56 raise Exception("Incorrect SILAC specification. Use medium only together with light and heavy labels.")
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57 multiplicity = 3 if medium_labels else 2 if heavy_labels else 1
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58 max_label = str(max(len(light_labels) if light_labels else 0,
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59 len(medium_labels) if medium_labels else 0,
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60 len(heavy_labels) if heavy_labels else 0))
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61 self._root.find('multiplicity').text = str(multiplicity)
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62 self._root.find('maxLabeledAa').text = max_label
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63 node = self._root.find('labelMods')
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64 node[0].text = ';'.join(light_labels) if light_labels else ''
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65 if multiplicity == 3:
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66 et_add_child(node, name='string', text=';'.join(medium_labels))
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67 if multiplicity > 1:
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68 et_add_child(node, name='string',
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69 text=';'.join(heavy_labels) if heavy_labels else '')
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70
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71 def set_isobaric_label(self, internalLabel, terminalLabel,
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72 cm2, cm1, cp1, cp2, tmtLike):
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73 """Add isobaric label info.
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74 Args:
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75 internalLabel: string
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76 terminalLabel: string
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77 cm2: (float) correction factor
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78 cm1: (float) correction factor
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79 cp1: (float) correction factor
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80 cp2: (float) correction factor
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81 tmtLike: bool or string
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82 Returns:
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83 None
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84 """
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85 iso_labels_node = self._root.find('isobaricLabels')
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86 label = et_add_child(iso_labels_node, 'IsobaricLabelInfo', '')
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87 et_add_child(label, 'internalLabel', internalLabel)
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88 et_add_child(label, 'terminalLabel', terminalLabel)
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89 for num, factor in (('M2', cm2), ('M1', cm1), ('P1', cp1), ('P2', cp2)):
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90 et_add_child(label, 'correctionFactor' + num,
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91 str(float(factor) if factor % 1 else int(factor)))
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92 et_add_child(label, 'tmtLike', str(tmtLike))
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93
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94
0
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95 class MQParam:
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96 """Represents a mqpar.xml and provides methods to modify
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97 some of its parameters.
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98 """
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99
3
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100 def __init__(self, mqpar_in, exp_design=None, yaml=None, substitution_rx=r'[^\s\S]'): # no sub by default
0
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101 """Initialize MQParam class. mqpar_in can either be a template
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102 or a already suitable mqpar file.
3
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103 Args:
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104 mqpar_in: a template parameter file
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105 exp_design: a experimental design template (see MaxQuant documentation),
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106 can be None
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107 substitution_rx: a regular expression for replacements in the file names.
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108 It is applied before comparing input file names (e.g. from the exp. design)
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109 """
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110 self.orig_mqpar = mqpar_in
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111 self.exp_design = exp_design
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112 self._root = ET.parse(mqpar_in).getroot()
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113 self.version = self._root.find('maxQuantVersion').text
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114 # regex for substitution of certain file name characters
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115 self.substitution_rx = substitution_rx
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116 self.pg_node = copy.deepcopy(self._root.find('parameterGroups')[0])
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117 self._paramGroups = []
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118 self.fasta_file_node = copy.deepcopy(self._root.find('fastaFiles')[0])
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119 if yaml:
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120 self._from_yaml(yaml)
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121
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122 def __getitem__(self, index):
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123 """Return paramGroup if indexed with integer, else try to find
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124 matching Element in XML root and return its text or None.
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125 """
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126 try:
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127 return self._paramGroups[index]
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128 except TypeError:
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129 ret = self._root.find(index)
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130 return ret.text if ret is not None else None
0
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131
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132 @staticmethod
3
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133 def _check_validity(design, len_infiles):
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134 """Perform some checks on the exp. design template"""
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135 design_len = len(design['Name'])
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136 # 'Name' can be None, we need at least len_infiles valid entries
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137 match = len(list(filter(lambda x: bool(x), design['Name'])))
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138 if match < len_infiles:
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139 raise Exception(' '.join(["Error parsing experimental design template:",
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140 "Found only {} matching entries".format(match),
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141 "for {} input files".format(len_infiles)]))
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142 for i in range(0, design_len):
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143 msg = "(in line " + str(i + 2) + " of experimental design) "
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144 if not design['Experiment'][i]:
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145 raise ValueError(msg + " Experiment is empty.")
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146 if design['PTM'][i].lower() not in ('true', 'false'):
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147 raise ValueError(msg + "Defines invalid PTM value, should be 'True' or 'False'.")
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148 try:
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149 int(design['Fraction'][i])
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150 except ValueError as e:
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151 raise ValueError(msg + str(e))
0
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152
3
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153 def _make_exp_design(self, groups, files):
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154 """Create a dict representing an experimental design from an
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155 experimental design template and a list input files.
0
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156 If the experimental design template is None, create a default
3
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157 design with one experiment for each input file and no fractions
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158 for all files.
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159 Args:
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160 files: list of input file paths
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161 groups: list of parameter group indices
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162 Returns:
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163 dict: The (complete) experimental design template
0
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164 """
3
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165 design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment", "paramGroup")}
0
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166 if not self.exp_design:
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167 design["Name"] = files
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168 design["Fraction"] = ('32767',) * len(files)
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169 design["Experiment"] = [os.path.split(f)[1] for f in files]
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170 design["PTM"] = ('False',) * len(files)
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171 design["paramGroup"] = groups
0
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172 else:
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173 with open(self.exp_design) as design_file:
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174 index_line = design_file.readline().strip()
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175 index = []
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176 for i in index_line.split('\t'):
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177 if i in design:
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178 index.append(i)
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179 else:
3
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180 raise Exception("Invalid column index in experimental design template: {}".format(i))
0
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181 for line in design_file:
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182 row = line.strip().split('\t')
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183 for e, i in zip_longest(row, index):
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184 if i == "Fraction" and not e:
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185 e = '32767'
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186 elif i == "PTM" and not e:
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187 e = 'False'
0
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188 design[i].append(e)
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189 # map files to names in exp. design template
0
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190 names = []
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191 names_to_paths = {}
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192 # strip path and extension
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193 for f in files:
0
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194 b = os.path.basename(f)
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195 basename = b[:-11] if b.lower().endswith('.thermo.raw') else b.rsplit('.', maxsplit=1)[0]
0
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196 names_to_paths[basename] = f
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197 for name in design['Name']:
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198 # same substitution as in maxquant.xml,
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199 # when passing the element identifiers
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200 fname = re.sub(self.substitution_rx, '_', name)
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201 names.append(names_to_paths[fname] if fname in names_to_paths
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202 else None)
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203 # replace orig. file names with matching links to galaxy datasets
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204 design['Name'] = names
3
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205 design['paramGroup'] = groups
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206 MQParam._check_validity(design, len(files))
0
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207 return design
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208
3
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209 def add_infiles(self, infiles):
0
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210 """Add a list of raw/mzxml files to the mqpar.xml.
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211 If experimental design template was specified,
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212 modify other parameters accordingly.
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213 The files must be specified as absolute paths
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214 for maxquant to find them.
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215 Also add parameter Groups.
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216 Args:
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217 infiles: a list of infile lists. first dimension denotes the
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218 parameter group.
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219 Returns:
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220 None
0
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221 """
3
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222 groups, files = zip(*[(num, f) for num, l in enumerate(infiles) for f in l])
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223 self._paramGroups = [ParamGroup(self.pg_node) for i in range(len(infiles))]
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224 nodenames = ('filePaths', 'experiments', 'fractions',
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225 'ptms', 'paramGroupIndices', 'referenceChannel')
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226 design = self._make_exp_design(groups, files)
0
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227 # Get parent nodes from document
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228 nodes = dict()
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229 for nodename in nodenames:
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230 node = self._root.find(nodename)
0
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231 if node is None:
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232 raise ValueError('Element {} not found in parameter file'
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233 .format(nodename))
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234 nodes[nodename] = node
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235 node.clear()
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236 node.tag = nodename
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237 # Append sub-elements to nodes (one per file)
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238 for i, name in enumerate(design['Name']):
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239 if name:
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240 et_add_child(nodes['filePaths'], 'string', name)
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241 et_add_child(nodes['experiments'], 'string',
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242 design['Experiment'][i])
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243 et_add_child(nodes['fractions'], 'short',
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244 design['Fraction'][i])
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245 et_add_child(nodes['ptms'], 'boolean',
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246 design['PTM'][i])
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247 et_add_child(nodes['paramGroupIndices'], 'int',
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248 design['paramGroup'][i])
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249 et_add_child(nodes['referenceChannel'], 'string', '')
0
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250
3
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251 def translate(self, infiles):
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252 """Map a list of given infiles to the files specified in the parameter file.
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253 Needed for the mqpar upload in galaxy. Removes the path and then tries
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254 to match the files.
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255 Args:
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256 infiles: list or tuple of the input
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257 Returns:
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258 None
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259 """
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260 # kind of a BUG: fails if filename starts with '.'
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261 infilenames = [os.path.basename(f).split('.')[0] for f in infiles]
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262 filesNode = self._root.find('filePaths')
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263 files_from_mqpar = [e.text for e in filesNode]
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264 filesNode.clear()
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265 filesNode.tag = 'filePaths'
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266 for f in files_from_mqpar:
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267 # either windows or posix path
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268 win = ntpath.basename(f)
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269 posix = os.path.basename(f)
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270 basename = win if len(win) < len(posix) else posix
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271 basename_with_sub = re.sub(self.substitution_rx, '_',
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272 basename.split('.')[0])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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273 # match infiles to their names in mqpar.xml,
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274 # ignore files missing in mqpar.xml
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275 if basename_with_sub in infilenames:
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276 i = infilenames.index(basename_with_sub)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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277 et_add_child(filesNode, 'string', infiles[i])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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278 else:
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279 raise ValueError("no matching infile found for " + f)
0
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280
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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281 def add_fasta_files(self, files, parse_rules={}):
0
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282 """Add fasta file groups.
3
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283 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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284 files: (list) of fasta file paths
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285 parseRules: (dict) the parse rules as (tag, text)-pairs
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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286 Returns:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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287 None
0
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288 """
3
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289 fasta_node = self._root.find('fastaFiles')
0
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290 fasta_node.clear()
3
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291 for f in files:
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292 fasta_node.append(copy.deepcopy(self.fasta_file_node))
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293 fasta_node[-1].find('fastaFilePath').text = f
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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294 for rule in parse_rules:
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295 fasta_node[-1].find(rule).text = parse_rules[rule]
0
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296
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297 def set_simple_param(self, key, value):
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298 """Set a simple parameter.
3
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299 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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300 key: (string) XML tag of the parameter
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301 value: the text of the parameter XML node
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302 Returns:
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303 None
0
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304 """
3
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305 node = self._root.find(key)
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306 if node is None:
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307 raise ValueError('Element {} not found in parameter file'
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308 .format(key))
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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309 node.text = str(value)
0
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310
3
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311 def _from_yaml(self, conf):
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312 """Read a yaml config file.
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313 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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314 conf: (string) path to the yaml conf file
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315 Returns:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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316 None
0
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317 """
3
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318 with open(conf) as f:
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319 conf_dict = yaml.safe_load(f.read())
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320 paramGroups = conf_dict.pop('paramGroups')
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321 self.add_infiles([pg.pop('files') for pg in paramGroups])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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322 for i, pg in enumerate(paramGroups):
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323 silac = pg.pop('labelMods', False)
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324 if silac:
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325 self[i].set_silac(*silac)
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326 isobaricLabels = pg.pop('isobaricLabels', False)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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327 if isobaricLabels:
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328 for l in isobaricLabels:
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329 self[i].set_isobaric_label(*l)
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330 for el in ['fixedModifications', 'variableModifications', 'enzymes']:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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331 lst = pg.pop(el, None)
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332 if lst is not None:
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333 self[i].set_list_param(el, lst)
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334 for key in pg:
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335 self[i].set_simple_param(key, pg[key])
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336 fastafiles = conf_dict.pop('fastaFiles', False)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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337 if fastafiles:
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338 self.add_fasta_files(fastafiles, parse_rules=conf_dict.pop('parseRules', {}))
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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339 else:
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340 raise Exception('No fasta files provided.')
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341 for key in conf_dict:
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342 self.set_simple_param(key, conf_dict[key])
0
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343
3
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344 def write(self, mqpar_out):
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345 """Write pretty formatted xml parameter file.
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346 Compose it from global parameters and parameter Groups.
0
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347 """
3
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348 if self._paramGroups:
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349 pg_node = self._root.find('parameterGroups')
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350 pg_node.remove(pg_node[0])
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351 for group in self._paramGroups:
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352 pg_node.append(group._root)
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galaxyp
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diff changeset
353 rough_string = ET.tostring(self._root, 'utf-8', short_empty_elements=False)
0
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354 reparsed = minidom.parseString(rough_string)
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355 pretty = reparsed.toprettyxml(indent="\t")
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galaxyp
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356 even_prettier = re.sub(r"\n\s+\n", r"\n", pretty)
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
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diff changeset
357 with open(mqpar_out, 'w') as f:
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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358 print(even_prettier, file=f)