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1 #!/usr/bin/env python
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2 """
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3 Usage:
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4 python augment_maxquant_mods.py
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5
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6 Assuming Unimod XML file (unimod.xml) and stock MaxQuant modifications
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7 file (modifications.xml) are in this same directory, this script will
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8 create a new MaxQuant modifications file (extended_modifications.xml)
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9 with an a new modification for each unimod entry. These new entires
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10 will be suffixed with [Unimod] to distinguish them from existing
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11 MaxQuant entries. This file should be copied to
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12 <MaxQuant Path>\bin\conf\modifications.xml
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13
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14 """
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15 import xml.etree.ElementTree as ET
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16 import re
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17
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18 FAKE_DATE = "2012-06-11T21:21:24.4946343+02:00"
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19
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20 POSITION_MAP = {
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21 "Anywhere": "anywhere",
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22 "Any N-term": "anyNterm",
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23 "Any C-term": "anyCterm",
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24 "Protein N-term": "proteinNterm",
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25 "Protein C-term": "proteinCterm",
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26 }
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27
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28 unimod_tree = ET.parse('unimod.xml')
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29 unimod_ns = '{http://www.unimod.org/xmlns/schema/unimod_2}'
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30 unimod_modifications_el = unimod_tree.getroot().find('%smodifications' % unimod_ns)
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31 mq_tree = ET.parse("modifications.xml")
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32 mq_root = mq_tree.getroot()
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33
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34
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35 def to_label(title, site):
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36 return "%s (%s) [Unimod]" % (title, site)
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37
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38
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39 def copy_modification(unimod_modification):
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40 if unimod_modification.hidden:
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41 return False
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42 if unimod_modification.delta_el is None:
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43 return False
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44 comp_array = unimod_modification.composition_array
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45 for aa, count in comp_array:
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46 if len(aa) > 1 and aa not in COMP_REPLACES.keys():
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47 # Complex stuff like Hep, that I cannot translate into MaxQuant.
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48 return False
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49 return True
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50
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51
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52 COMP_REPLACES = {
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53 "15N": "Nx",
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54 "13C": "Cx",
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55 "18O": "Ox",
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56 "2H": "Hx",
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57 }
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58
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59 ## HEP?
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60
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61
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62 def convert_composition(unimod_composition):
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63 """
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64 Convert Unimod representation of composition to MaxQuant
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65 """
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66 composition = unimod_composition
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67 for key, value in COMP_REPLACES.iteritems():
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68 composition = composition.replace(key, value)
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69 print composition
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70 return composition
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71
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72
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73 def populate_modification(modification, unimod_modification):
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74 """
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75 Copy unimod entry ``unimod_modification`` to MaxQuant entry ``modification``.
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76 """
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77 attrib = modification.attrib
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78 attrib["create_date"] = FAKE_DATE
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79 attrib["last_modified_date"] = FAKE_DATE
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80 attrib["reporterCorrectionM1"] = str(0)
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81 attrib["reporterCorrectionM2"] = str(0)
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82 attrib["reporterCorrectionP1"] = str(0)
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83 attrib["reporterCorrectionP2"] = str(0)
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84 attrib["user"] = "build_mods_script"
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85 label = unimod_modification.label
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86 attrib["title"] = label
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87 attrib["description"] = label
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88 attrib["composition"] = convert_composition(unimod_modification.raw_composition)
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89 unimod_position = unimod_modification.position
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90 maxquant_position = POSITION_MAP[unimod_position]
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91 assert maxquant_position != None
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92 position_el = ET.SubElement(modification, "position")
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93 position_el.text = maxquant_position
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94 modification_site_el = ET.SubElement(modification, "modification_site")
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95 modification_site_el.attrib["index"] = "0"
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96 unimod_site = unimod_modification.site
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97 modification_site_el.attrib["site"] = "-" if len(unimod_site) > 1 else unimod_site
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98 type_el = ET.SubElement(modification, "type")
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99 type_el.text = "standard"
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100 return modification
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101
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102
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103 class UnimodModification:
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104
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105 def __init__(self, modification, specificity):
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106 self.modification = modification
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107 self.specificity = specificity
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108
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109 @property
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110 def title(self):
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111 return self.modification.attrib["title"]
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112
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113 @property
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114 def site(self):
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115 return self.specificity.attrib["site"]
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116
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117 @property
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118 def label(self):
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119 return "%s (%s) [Unimod]" % (self.title, self.site)
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120
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121 @property
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122 def delta_el(self):
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123 return self.modification.find("%sdelta" % unimod_ns)
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124
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125 @property
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126 def raw_composition(self):
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127 return self.delta_el.attrib["composition"]
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128
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129 @property
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130 def composition_array(self):
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131 raw_composition = self.raw_composition
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132 aa_and_counts = re.split("\s+", raw_composition)
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133 comp_array = []
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134 for aa_and_count in aa_and_counts:
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135 match = re.match(r"(\w+)(\((-?\d+)\))?", aa_and_count)
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136 aa = match.group(1)
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137 count = match.group(3) or 1
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138 comp_array.append((aa, count))
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139 return comp_array
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140
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141 @property
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142 def position(self):
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143 return self.specificity.attrib["position"]
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144
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145 @property
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146 def hidden(self):
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147 return self.specificity.attrib["hidden"] == "true"
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148
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149 unimod_modifications = []
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150 for mod in unimod_modifications_el.findall('%smod' % unimod_ns):
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151 for specificity in mod.findall('%sspecificity' % unimod_ns):
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152 unimod_modifications.append(UnimodModification(mod, specificity))
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153
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154 max_index = 0
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155 for modification in mq_root.getchildren():
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156 index = int(modification.attrib["index"])
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157 max_index = max(max_index, index)
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158
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159 for unimod_modification in unimod_modifications:
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160 if copy_modification(unimod_modification):
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161 print unimod_modification.composition_array
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162 max_index += 1
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163 modification = ET.SubElement(mq_root, "modification", attrib={"index": str(max_index)})
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164 populate_modification(modification, unimod_modification)
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165
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166 mq_tree.write("extended_modifications.xml")
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