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1 #!/usr/bin/env python
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2 # encoding: utf-8
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3 '''
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4 Module to combine output from the GCMS Galaxy tools RankFilter, CasLookup and MsClust
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5 into a tabular file that can be uploaded to the MetExp database.
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6
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7 RankFilter, CasLookup are already combined by combine_output.py so here we will use
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8 this result. Furthermore here one of the MsClust
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9 quantification files containing the respective spectra details are to be combined as well.
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10
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11 Extra calculations performed:
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12 - The column MW is also added here and is derived from the column FORMULA found
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13 in RankFilter, CasLookup combined result.
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14
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15 So in total here we merge 2 files and calculate one new column.
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16 '''
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17 from pkg_resources import resource_filename # @UnresolvedImport # pylint: disable=E0611
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18 import csv
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19 import re
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20 import sys
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21 from collections import OrderedDict
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22
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23 __author__ = "Pieter Lukasse"
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24 __contact__ = "pieter.lukasse@wur.nl"
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25 __copyright__ = "Copyright, 2013, Plant Research International, WUR"
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26 __license__ = "Apache v2"
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27
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28 def _process_data(in_csv, delim='\t'):
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29 '''
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30 Generic method to parse a tab-separated file returning a dictionary with named columns
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31 @param in_csv: input filename to be parsed
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32 '''
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33 data = list(csv.reader(open(in_csv, 'rU'), delimiter=delim))
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34 header = data.pop(0)
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35 # Create dictionary with column name as key
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36 output = OrderedDict()
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37 for index in xrange(len(header)):
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38 output[header[index]] = [row[index] for row in data]
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39 return output
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40
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41 ONE_TO_ONE = 'one_to_one'
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42 N_TO_ONE = 'n_to_one'
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43
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44 def _merge_data(set1, link_field_set1, set2, link_field_set2, compare_function, merge_function, metadata, relation_type=ONE_TO_ONE):
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45 '''
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46 Merges data from both input dictionaries based on the link fields. This method will
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47 build up a new list containing the merged hits as the items.
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48 @param set1: dictionary holding set1 in the form of N lists (one list per attribute name)
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49 @param set2: dictionary holding set2 in the form of N lists (one list per attribute name)
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50 '''
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51 # TODO test for correct input files -> same link_field values should be there
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52 # (test at least number of unique link_field values):
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53 #
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54 # if (len(set1[link_field_set1]) != len(set2[link_field_set2])):
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55 # raise Exception('input files should have the same nr of key values ')
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56
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57
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58 merged = []
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59 processed = {}
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60 for link_field_set1_idx in xrange(len(set1[link_field_set1])):
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61 link_field_set1_value = set1[link_field_set1][link_field_set1_idx]
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62 if not link_field_set1_value in processed :
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63 # keep track of processed items to not repeat them
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64 processed[link_field_set1_value] = link_field_set1_value
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65
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66 # Get the indices for current link_field_set1_value in both data-structures for proper matching
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67 set1index = [index for index, value in enumerate(set1[link_field_set1]) if value == link_field_set1_value]
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68 set2index = [index for index, value in enumerate(set2[link_field_set2]) if compare_function(value, link_field_set1_value)==True ]
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69 # Validation :
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70 if len(set2index) == 0:
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71 # means that corresponding data could not be found in set2, then throw error
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72 raise Exception("Datasets not compatible, merge not possible. " + link_field_set1 + "=" +
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73 link_field_set1_value + " only found in first dataset. ")
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74
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75 merged_hits = []
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76 # Combine hits
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77 for hit in xrange(len(set1index)):
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78 # Create records of hits to be merged ("keys" are the attribute names, so what the lines below do
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79 # is create a new "dict" item with same "keys"/attributes, with each attribute filled with its
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80 # corresponding value in the sets; i.e.
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81 # set1[key] => returns the list/array with size = nrrows, with the values for the attribute
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82 # represented by "key".
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83 # set1index[hit] => points to the row nr=hit (hit is a rownr/index)
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84 # So set1[x][set1index[n]] = set1.attributeX.instanceN
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85 #
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86 # It just ensures the entry is made available as a plain named array for easy access.
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87 rf_record = OrderedDict(zip(set1.keys(), [set1[key][set1index[hit]] for key in set1.keys()]))
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88 if relation_type == ONE_TO_ONE :
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89 cl_record = OrderedDict(zip(set2.keys(), [set2[key][set2index[hit]] for key in set2.keys()]))
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90 else:
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91 # is N to 1:
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92 cl_record = OrderedDict(zip(set2.keys(), [set2[key][set2index[0]] for key in set2.keys()]))
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93
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94 merged_hit = merge_function(rf_record, cl_record, metadata)
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95 merged_hits.append(merged_hit)
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96
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97 merged.append(merged_hits)
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98
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99 return merged, len(set1index)
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100
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101
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102 def _compare_records(key1, key2):
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103 '''
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104 in this case the compare method is really simple as both keys are expected to contain
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105 same value when records are the same
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106 '''
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107 if key1 == key2:
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108 return True
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109 else:
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110 return False
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111
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112
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113
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114 def _merge_records(rank_caslookup_combi, msclust_quant_record, metadata):
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115 '''
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116 Combines single records from both the RankFilter+CasLookup combi file and from MsClust file
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117
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118 @param rank_caslookup_combi: rankfilter and caslookup combined record (see combine_output.py)
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119 @param msclust_quant_record: msclust quantification + spectrum record
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120 '''
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121 record = []
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122 for column in rank_caslookup_combi:
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123 record.append(rank_caslookup_combi[column])
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124
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125 for column in msclust_quant_record:
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126 record.append(msclust_quant_record[column])
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127
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128 for column in metadata:
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129 record.append(metadata[column])
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130
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131 # add MOLECULAR MASS (MM)
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132 molecular_mass = get_molecular_mass(rank_caslookup_combi['FORMULA'])
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133 # limit to two decimals:
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134 record.append("{0:.2f}".format(molecular_mass))
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135
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136 # add MOLECULAR WEIGHT (MW) - TODO - calculate this
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137 record.append('0.0')
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138
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139 # level of identification and Location of reference standard
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140 record.append('0')
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141 record.append('')
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142
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143 return record
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144
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145
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146 def get_molecular_mass(formula):
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147 '''
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148 Calculates the molecular mass (MM).
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149 E.g. MM of H2O = (relative)atomic mass of H x2 + (relative)atomic mass of O
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150 '''
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151
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152 # Each element is represented by a capital letter, followed optionally by
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153 # lower case, with one or more digits as for how many elements:
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154 element_pattern = re.compile("([A-Z][a-z]?)(\d*)")
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155
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156 total_mass = 0
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157 for (element_name, count) in element_pattern.findall(formula):
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158 if count == "":
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159 count = 1
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160 else:
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161 count = int(count)
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162 element_mass = float(elements_and_masses_map[element_name]) # "found: Python's built-in float type has double precision " (? check if really correct ?)
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163 total_mass += element_mass * count
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164
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165 return total_mass
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166
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167
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168
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169 def _save_data(data, headers, out_csv):
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170 '''
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171 Writes tab-separated data to file
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172 @param data: dictionary containing merged dataset
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173 @param out_csv: output csv file
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174 '''
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175
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176 # Open output file for writing
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177 outfile_single_handle = open(out_csv, 'wb')
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178 output_single_handle = csv.writer(outfile_single_handle, delimiter="\t")
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179
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180 # Write headers
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181 output_single_handle.writerow(headers)
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182
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183 # Write
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184 for item_idx in xrange(len(data)):
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185 for hit in data[item_idx]:
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186 output_single_handle.writerow(hit)
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187
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188
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189 def _get_map_for_elements_and_masses(elements_and_masses):
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190 '''
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191 This method will read out the column 'Chemical symbol' and make a map
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192 of this, storing the column 'Relative atomic mass' as its value
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193 '''
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194 resultMap = {}
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195 index = 0
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196 for entry in elements_and_masses['Chemical symbol']:
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197 resultMap[entry] = elements_and_masses['Relative atomic mass'][index]
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198 index += 1
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199
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200 return resultMap
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201
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202
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203 def init_elements_and_masses_map():
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204 '''
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205 Initializes the lookup map containing the elements and their respective masses
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206 '''
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207 elements_and_masses = _process_data(resource_filename(__name__, "static_resources/elements_and_masses.tab"))
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208 global elements_and_masses_map
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209 elements_and_masses_map = _get_map_for_elements_and_masses(elements_and_masses)
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210
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211
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212 def main():
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213 '''
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214 Combine Output main function
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215
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216 RankFilter, CasLookup are already combined by combine_output.py so here we will use
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217 this result. Furthermore here the MsClust spectra file (.MSP) and one of the MsClust
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218 quantification files are to be combined with combine_output.py result as well.
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219 '''
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220 rankfilter_and_caslookup_combined_file = sys.argv[1]
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221 msclust_quantification_and_spectra_file = sys.argv[2]
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222 output_csv = sys.argv[3]
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223 # metadata
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224 metadata = OrderedDict()
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225 metadata['organism'] = sys.argv[4]
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226 metadata['tissue'] = sys.argv[5]
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227 metadata['experiment_name'] = sys.argv[6]
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228 metadata['user_name'] = sys.argv[7]
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229 metadata['column_type'] = sys.argv[8]
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230
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231 # Read RankFilter and CasLookup output files
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232 rankfilter_and_caslookup_combined = _process_data(rankfilter_and_caslookup_combined_file)
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233 msclust_quantification_and_spectra = _process_data(msclust_quantification_and_spectra_file, ',')
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234
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235 # Read elements and masses to use for the MW/MM calculation :
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236 init_elements_and_masses_map()
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237
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238 merged, nhits = _merge_data(rankfilter_and_caslookup_combined, 'Centrotype',
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239 msclust_quantification_and_spectra, 'centrotype',
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240 _compare_records, _merge_records, metadata,
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241 N_TO_ONE)
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242 headers = rankfilter_and_caslookup_combined.keys() + msclust_quantification_and_spectra.keys() + metadata.keys() + ['MM','MW', 'Level of identification', 'Location of reference standard']
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243 _save_data(merged, headers, output_csv)
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244
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245
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246 if __name__ == '__main__':
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247 main()
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