Mercurial > repos > galaxyp > maxquant_mqpar

annotate mqparam.py @ 4:9cb7dcc07dae draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
author galaxyp
date Fri, 19 Feb 2021 21:25:06 +0000
parents 2d67fb758956
children
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256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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1 """
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2 Create a project-specific MaxQuant parameter file.
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3 """
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4
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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
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7 import os
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8 import re
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9 import xml.etree.ElementTree as ET
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10 from itertools import zip_longest
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11 from xml.dom import minidom
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12
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13 import yaml
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14
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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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16 def et_add_child(el, name, text, attrib=None):
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17 "Add a child element to an xml.etree.ElementTree.Element"
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18 child = ET.SubElement(el, name, attrib=attrib if attrib else {})
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19 child.text = str(text)
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20 return child
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23 class ParamGroup:
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24 """Represents one parameter Group
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25 """
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27 def __init__(self, root):
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28 """Initialize with its xml.etree.ElementTree root Element.
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29 """
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30 self._root = copy.deepcopy(root)
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32 def set_list_param(self, key, vals):
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33 """Set a list parameter.
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34 """
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35 node = self._root.find(key)
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36 if node is None:
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37 raise ValueError('Element {} not found in parameter file'
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38 .format(key))
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39 node.clear()
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40 node.tag = key
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41 for e in vals:
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42 et_add_child(node, name='string', text=e)
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43
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44 def set_simple_param(self, key, value):
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45 """Set a simple parameter.
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46 """
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47 node = self._root.find(key)
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48 if node is None:
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49 raise ValueError('Element {} not found in parameter file'
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50 .format(key))
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51 node.text = str(value)
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52
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53 def set_silac(self, light_labels, medium_labels, heavy_labels):
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54 """Set label modifications.
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55 """
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56 if medium_labels and not (heavy_labels or light_labels): # medium omly with heavy and light
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57 raise Exception("Incorrect SILAC specification. Use medium only together with light and heavy labels.")
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58 multiplicity = 3 if medium_labels else 2 if heavy_labels else 1
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59 max_label = str(max(len(light_labels) if light_labels else 0,
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60 len(medium_labels) if medium_labels else 0,
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61 len(heavy_labels) if heavy_labels else 0))
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62 self._root.find('multiplicity').text = str(multiplicity)
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63 self._root.find('maxLabeledAa').text = max_label
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64 node = self._root.find('labelMods')
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65 node[0].text = ';'.join(light_labels) if light_labels else ''
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66 if multiplicity == 3:
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67 et_add_child(node, name='string', text=';'.join(medium_labels))
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68 if multiplicity > 1:
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69 et_add_child(node, name='string',
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70 text=';'.join(heavy_labels) if heavy_labels else '')
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71
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72 def set_isobaric_label(self, internalLabel, terminalLabel,
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73 cm2, cm1, cp1, cp2, tmtLike):
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74 """Add isobaric label info.
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75 Args:
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76 internalLabel: string
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77 terminalLabel: string
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78 cm2: (float) correction factor
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79 cm1: (float) correction factor
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80 cp1: (float) correction factor
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81 cp2: (float) correction factor
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82 tmtLike: bool or string
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83 Returns:
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84 None
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85 """
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86 iso_labels_node = self._root.find('isobaricLabels')
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87 label = et_add_child(iso_labels_node, 'IsobaricLabelInfo', '')
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88 et_add_child(label, 'internalLabel', internalLabel)
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89 et_add_child(label, 'terminalLabel', terminalLabel)
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90 for num, factor in (('M2', cm2), ('M1', cm1), ('P1', cp1), ('P2', cp2)):
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91 et_add_child(label, 'correctionFactor' + num,
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92 str(float(factor) if factor % 1 else int(factor)))
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93 et_add_child(label, 'tmtLike', str(tmtLike))
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94
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95
0
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96 class MQParam:
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97 """Represents a mqpar.xml and provides methods to modify
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98 some of its parameters.
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99 """
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100
3
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101 def __init__(self, mqpar_in, exp_design=None, yaml=None, substitution_rx=r'[^\s\S]'): # no sub by default
0
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102 """Initialize MQParam class. mqpar_in can either be a template
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103 or a already suitable mqpar file.
3
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104 Args:
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105 mqpar_in: a template parameter file
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106 exp_design: a experimental design template (see MaxQuant documentation),
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107 can be None
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108 substitution_rx: a regular expression for replacements in the file names.
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109 It is applied before comparing input file names (e.g. from the exp. design)
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110 """
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111 self.orig_mqpar = mqpar_in
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112 self.exp_design = exp_design
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113 self._root = ET.parse(mqpar_in).getroot()
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114 self.version = self._root.find('maxQuantVersion').text
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115 # regex for substitution of certain file name characters
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116 self.substitution_rx = substitution_rx
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117 self.pg_node = copy.deepcopy(self._root.find('parameterGroups')[0])
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118 self._paramGroups = []
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119 self.fasta_file_node = copy.deepcopy(self._root.find('fastaFiles')[0])
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120 if yaml:
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121 self._from_yaml(yaml)
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122
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123 def __getitem__(self, index):
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124 """Return paramGroup if indexed with integer, else try to find
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125 matching Element in XML root and return its text or None.
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126 """
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127 try:
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128 return self._paramGroups[index]
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129 except TypeError:
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130 ret = self._root.find(index)
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131 return ret.text if ret is not None else None
0
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132
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133 @staticmethod
3
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134 def _check_validity(design, len_infiles):
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135 """Perform some checks on the exp. design template"""
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136 design_len = len(design['Name'])
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137 # 'Name' can be None, we need at least len_infiles valid entries
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138 match = len(list(filter(lambda x: bool(x), design['Name'])))
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139 if match < len_infiles:
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140 raise Exception(' '.join(["Error parsing experimental design template:",
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141 "Found only {} matching entries".format(match),
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142 "for {} input files".format(len_infiles)]))
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143 for i in range(0, design_len):
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144 msg = "(in line " + str(i + 2) + " of experimental design) "
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145 if not design['Experiment'][i]:
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146 raise ValueError(msg + " Experiment is empty.")
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147 if design['PTM'][i].lower() not in ('true', 'false'):
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148 raise ValueError(msg + "Defines invalid PTM value, should be 'True' or 'False'.")
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149 try:
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150 int(design['Fraction'][i])
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151 except ValueError as e:
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152 raise ValueError(msg + str(e))
0
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153
3
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154 def _make_exp_design(self, groups, files):
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155 """Create a dict representing an experimental design from an
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156 experimental design template and a list input files.
0
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157 If the experimental design template is None, create a default
3
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158 design with one experiment for each input file and no fractions
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159 for all files.
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160 Args:
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161 files: list of input file paths
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162 groups: list of parameter group indices
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163 Returns:
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164 dict: The (complete) experimental design template
0
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165 """
3
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166 design = {s: [] for s in ("Name", "PTM", "Fraction", "Experiment", "paramGroup")}
0
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167 if not self.exp_design:
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168 design["Name"] = files
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169 design["Fraction"] = ('32767',) * len(files)
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170 design["Experiment"] = [os.path.split(f)[1] for f in files]
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171 design["PTM"] = ('False',) * len(files)
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172 design["paramGroup"] = groups
0
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173 else:
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174 with open(self.exp_design) as design_file:
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175 index_line = design_file.readline().strip()
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176 index = []
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177 for i in index_line.split('\t'):
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178 if i in design:
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179 index.append(i)
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180 else:
3
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181 raise Exception("Invalid column index in experimental design template: {}".format(i))
0
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182 for line in design_file:
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183 row = line.strip().split('\t')
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184 for e, i in zip_longest(row, index):
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185 if i == "Fraction" and not e:
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186 e = '32767'
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187 elif i == "PTM" and not e:
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188 e = 'False'
0
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189 design[i].append(e)
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190 # map files to names in exp. design template
0
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191 names = []
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192 names_to_paths = {}
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193 # strip path and extension
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194 for f in files:
0
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195 b = os.path.basename(f)
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196 basename = b[:-11] if b.lower().endswith('.thermo.raw') else b.rsplit('.', maxsplit=1)[0]
0
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197 names_to_paths[basename] = f
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198 for name in design['Name']:
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199 # same substitution as in maxquant.xml,
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200 # when passing the element identifiers
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201 fname = re.sub(self.substitution_rx, '_', name)
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202 names.append(names_to_paths[fname] if fname in names_to_paths
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203 else None)
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204 # replace orig. file names with matching links to galaxy datasets
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205 design['Name'] = names
3
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206 design['paramGroup'] = groups
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207 MQParam._check_validity(design, len(files))
0
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208 return design
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209
3
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210 def add_infiles(self, infiles):
0
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211 """Add a list of raw/mzxml files to the mqpar.xml.
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212 If experimental design template was specified,
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213 modify other parameters accordingly.
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214 The files must be specified as absolute paths
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215 for maxquant to find them.
3
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216 Also add parameter Groups.
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217 Args:
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218 infiles: a list of infile lists. first dimension denotes the
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219 parameter group.
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220 Returns:
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221 None
0
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222 """
3
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223 groups, files = zip(*[(num, f) for num, l in enumerate(infiles) for f in l])
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224 self._paramGroups = [ParamGroup(self.pg_node) for i in range(len(infiles))]
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225 nodenames = ('filePaths', 'experiments', 'fractions',
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226 'ptms', 'paramGroupIndices', 'referenceChannel')
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227 design = self._make_exp_design(groups, files)
0
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228 # Get parent nodes from document
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229 nodes = dict()
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230 for nodename in nodenames:
3
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231 node = self._root.find(nodename)
0
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232 if node is None:
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233 raise ValueError('Element {} not found in parameter file'
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234 .format(nodename))
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235 nodes[nodename] = node
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236 node.clear()
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237 node.tag = nodename
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238 # Append sub-elements to nodes (one per file)
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239 for i, name in enumerate(design['Name']):
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240 if name:
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241 et_add_child(nodes['filePaths'], 'string', name)
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242 et_add_child(nodes['experiments'], 'string',
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243 design['Experiment'][i])
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244 et_add_child(nodes['fractions'], 'short',
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245 design['Fraction'][i])
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246 et_add_child(nodes['ptms'], 'boolean',
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247 design['PTM'][i])
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248 et_add_child(nodes['paramGroupIndices'], 'int',
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249 design['paramGroup'][i])
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250 et_add_child(nodes['referenceChannel'], 'string', '')
0
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251
3
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252 def translate(self, infiles):
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253 """Map a list of given infiles to the files specified in the parameter file.
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254 Needed for the mqpar upload in galaxy. Removes the path and then tries
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255 to match the files.
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256 Args:
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257 infiles: list or tuple of the input
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258 Returns:
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259 None
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260 """
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261 # kind of a BUG: fails if filename starts with '.'
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262 infilenames = [os.path.basename(f).split('.')[0] for f in infiles]
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263 filesNode = self._root.find('filePaths')
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264 files_from_mqpar = [e.text for e in filesNode]
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265 filesNode.clear()
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266 filesNode.tag = 'filePaths'
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267 for f in files_from_mqpar:
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268 # either windows or posix path
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269 win = ntpath.basename(f)
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270 posix = os.path.basename(f)
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diff changeset
271 basename = win if len(win) < len(posix) else posix
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
272 basename_with_sub = re.sub(self.substitution_rx, '_',
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
273 basename.split('.')[0])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
274 # match infiles to their names in mqpar.xml,
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
275 # ignore files missing in mqpar.xml
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
276 if basename_with_sub in infilenames:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
277 i = infilenames.index(basename_with_sub)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
278 et_add_child(filesNode, 'string', infiles[i])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
279 else:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
280 raise ValueError("no matching infile found for " + f)
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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diff changeset
281
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
282 def add_fasta_files(self, files, parse_rules={}):
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
283 """Add fasta file groups.
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
284 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
285 files: (list) of fasta file paths
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
286 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"
galaxyp
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diff changeset
287 Returns:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
288 None
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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289 """
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
290 fasta_node = self._root.find('fastaFiles')
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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291 fasta_node.clear()
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
292 for f in files:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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diff changeset
293 fasta_node.append(copy.deepcopy(self.fasta_file_node))
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
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294 fasta_node[-1].find('fastaFilePath').text = f
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
295 for rule in parse_rules:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
296 fasta_node[-1].find(rule).text = parse_rules[rule]
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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297
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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298 def set_simple_param(self, key, value):
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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299 """Set a simple parameter.
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
300 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
301 key: (string) XML tag of the parameter
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
302 value: the text of the parameter XML node
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
303 Returns:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
304 None
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
305 """
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
306 node = self._root.find(key)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
307 if node is None:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
308 raise ValueError('Element {} not found in parameter file'
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
309 .format(key))
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
310 node.text = str(value)
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
311
4
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
312 def set_list_param(self, key, values):
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
313 """Set a list parameter.
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
314 Args:
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
315 key: (string) XML tag of the parameter
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
316 values: the lit of values of the parameter XML node
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
317 Returns:
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
318 None
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
319 """
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
320 node = self._root.find(key)
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
321 if node is None:
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
322 raise ValueError('Element {} not found in parameter file'
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
323 .format(key))
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
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diff changeset
324 node.clear()
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
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diff changeset
325 node.tag = key
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
326 for e in values:
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
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diff changeset
327 et_add_child(node, name='string', text=e)
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
328
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
329 def _from_yaml(self, conf):
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
330 """Read a yaml config file.
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
331 Args:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
332 conf: (string) path to the yaml conf file
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
333 Returns:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
334 None
0
256cc0e17454 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
diff changeset
335 """
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
336 with open(conf) as f:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
337 conf_dict = yaml.safe_load(f.read())
4
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
338
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
339 paramGroups = conf_dict.pop('paramGroups')
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
340 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"
galaxyp
parents: 0
diff changeset
341 for i, pg in enumerate(paramGroups):
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
342 silac = pg.pop('labelMods', False)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
343 if silac:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
344 self[i].set_silac(*silac)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
345 isobaricLabels = pg.pop('isobaricLabels', False)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
346 if isobaricLabels:
4
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
347 for ibl in isobaricLabels:
9cb7dcc07dae "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"
galaxyp
parents: 3
diff changeset
348 self[i].set_isobaric_label(*ibl)
3
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
349 for el in ['fixedModifications', 'variableModifications', 'enzymes']:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
350 lst = pg.pop(el, None)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
351 if lst is not None:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
352 self[i].set_list_param(el, lst)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
353 for key in pg:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
354 self[i].set_simple_param(key, pg[key])
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
355 fastafiles = conf_dict.pop('fastaFiles', False)
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
356 if fastafiles:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
357 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"
galaxyp
parents: 0
diff changeset
358 else:
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
359 raise Exception('No fasta files provided.')
2d67fb758956 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit da342a782ccc391b87fb4fead956b7b3cbd21258"
galaxyp
parents: 0
diff changeset
360 for key in conf_dict:
4
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361 if key in ['restrictMods']:
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362 self.set_list_param(key, conf_dict[key])
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363 else:
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364 self.set_simple_param(key, conf_dict[key])
0
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365
3
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366 def write(self, mqpar_out):
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367 """Write pretty formatted xml parameter file.
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368 Compose it from global parameters and parameter Groups.
0
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369 """
3
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370 if self._paramGroups:
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371 pg_node = self._root.find('parameterGroups')
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372 pg_node.remove(pg_node[0])
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373 for group in self._paramGroups:
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374 pg_node.append(group._root)
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375 rough_string = ET.tostring(self._root, 'utf-8', short_empty_elements=False)
0
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376 reparsed = minidom.parseString(rough_string)
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377 pretty = reparsed.toprettyxml(indent="\t")
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378 even_prettier = re.sub(r"\n\s+\n", r"\n", pretty)
3
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379 with open(mqpar_out, 'w') as f:
0
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380 print(even_prettier, file=f)