Mercurial > repos > pieterlukasse > prims_metabolomics

annotate query_metexp.py @ 57:963684611ccb

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fix for xcms support in msclust
author pieter.lukasse@wur.nl
date Fri, 12 Dec 2014 12:06:36 +0100
parents cd4f13119afa
children
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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 query a set of identifications against the METabolomics EXPlorer database.
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5
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6 It will take the input file and for each record it will query the
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7 molecular mass in the selected MetExp DB. If one or more compounds are found in the
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8 MetExp DB then extra information regarding these compounds is added to the output file.
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9
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10 The output file is thus the input file enriched with information about
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11 related items found in the selected MetExp DB.
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12 '''
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13 import csv
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14 import sys
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15 import fileinput
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16 import urllib2
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17 import time
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18 from collections import OrderedDict
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19
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20 __author__ = "Pieter Lukasse"
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21 __contact__ = "pieter.lukasse@wur.nl"
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22 __copyright__ = "Copyright, 2014, Plant Research International, WUR"
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23 __license__ = "Apache v2"
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24
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25 def _process_file(in_xsv, delim='\t'):
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26 '''
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27 Generic method to parse a tab-separated file returning a dictionary with named columns
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28 @param in_csv: input filename to be parsed
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29 '''
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30 data = list(csv.reader(open(in_xsv, 'rU'), delimiter=delim))
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31 return _process_data(data)
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32
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33 def _process_data(data):
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34
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35 header = data.pop(0)
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36 # Create dictionary with column name as key
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37 output = OrderedDict()
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38 for index in xrange(len(header)):
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39 output[header[index]] = [row[index] for row in data]
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40 return output
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41
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42
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43 def _query_and_add_data(input_data, casid_col, formula_col, molecular_mass_col, metexp_dblink, separation_method):
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44 '''
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45 This method will iterate over the record in the input_data and
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46 will enrich them with the related information found (if any) in the
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47 MetExp Database.
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48
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49 # TODO : could optimize this with multi-threading, see also nice example at http://stackoverflow.com/questions/2846653/python-multithreading-for-dummies
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50 '''
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51 merged = []
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52
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53 for i in xrange(len(input_data[input_data.keys()[0]])):
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54 # Get the record in same dictionary format as input_data, but containing
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55 # a value at each column instead of a list of all values of all records:
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56 input_data_record = OrderedDict(zip(input_data.keys(), [input_data[key][i] for key in input_data.keys()]))
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57
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58 # read the molecular mass and formula:
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59 cas_id = input_data_record[casid_col]
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60 formula = input_data_record[formula_col]
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61 molecular_mass = input_data_record[molecular_mass_col]
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62
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63 # search for related records in MetExp:
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64 data_found = None
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65 if cas_id != "undef":
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66 # 1- search for other experiments where this CAS id has been found:
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67 query_link = metexp_dblink + "/find_entries/query?cas_nr="+ cas_id + "&method=" + separation_method
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68 data_found = _fire_query_and_return_dict(query_link + "&_format_result=tsv")
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69 data_type_found = "CAS"
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70 if data_found == None:
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71 # 2- search for other experiments where this FORMULA has been found:
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72 query_link = metexp_dblink + "/find_entries/query?molecule_formula="+ formula + "&method=" + separation_method
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73 data_found = _fire_query_and_return_dict(query_link + "&_format_result=tsv")
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74 data_type_found = "FORMULA"
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75 if data_found == None:
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76 # 3- search for other experiments where this MM has been found:
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77 query_link = metexp_dblink + "/find_entries/query?molecule_mass="+ molecular_mass + "&method=" + separation_method
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78 data_found = _fire_query_and_return_dict(query_link + "&_format_result=tsv")
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79 data_type_found = "MM"
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80
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81 if data_found == None:
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82 # If still nothing found, just add empty columns
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83 extra_cols = ['', '','','','','','','']
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84 else:
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85 # Add info found:
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86 extra_cols = _get_extra_info_and_link_cols(data_found, data_type_found, query_link)
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87
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88 # Take all data and merge it into a "flat"/simple array of values:
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89 field_values_list = _merge_data(input_data_record, extra_cols)
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90
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91 merged.append(field_values_list)
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92
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93 # return the merged/enriched records:
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94 return merged
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95
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96
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97 def _get_extra_info_and_link_cols(data_found, data_type_found, query_link):
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98 '''
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99 This method will go over the data found and will return a
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100 list with the following items:
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101 - Experiment details where hits have been found :
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102 'organism', 'tissue','experiment_name','user_name','column_type'
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103 - Link that executes same query
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104
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105 '''
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106 # set() makes a unique list:
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107 organism_set = []
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108 tissue_set = []
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109 experiment_name_set = []
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110 user_name_set = []
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111 column_type_set = []
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112 cas_nr_set = []
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113
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114 if 'organism' in data_found:
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115 organism_set = set(data_found['organism'])
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116 if 'tissue' in data_found:
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117 tissue_set = set(data_found['tissue'])
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118 if 'experiment_name' in data_found:
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119 experiment_name_set = set(data_found['experiment_name'])
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120 if 'user_name' in data_found:
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121 user_name_set = set(data_found['user_name'])
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122 if 'column_type' in data_found:
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123 column_type_set = set(data_found['column_type'])
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124 if 'CAS' in data_found:
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125 cas_nr_set = set(data_found['CAS'])
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126
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127
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128 result = [data_type_found,
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129 _to_xsv(organism_set),
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130 _to_xsv(tissue_set),
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131 _to_xsv(experiment_name_set),
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132 _to_xsv(user_name_set),
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133 _to_xsv(column_type_set),
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134 _to_xsv(cas_nr_set),
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135 #To let Excel interpret as link, use e.g. =HYPERLINK("http://stackoverflow.com", "friendly name"):
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136 "=HYPERLINK(\""+ query_link + "\", \"Link to entries found in DB \")"]
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137 return result
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138
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139
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140 def _to_xsv(data_set):
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141 result = ""
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142 for item in data_set:
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143 result = result + str(item) + "|"
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144 return result
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145
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146
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147 def _fire_query_and_return_dict(url):
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148 '''
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149 This method will fire the query as a web-service call and
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150 return the results as a list of dictionary objects
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151 '''
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152
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153 try:
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154 data = urllib2.urlopen(url).read()
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155
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156 # transform to dictionary:
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157 result = []
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158 data_rows = data.split("\n")
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159
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160 # check if there is any data in the response:
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161 if len(data_rows) <= 1 or data_rows[1].strip() == '':
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162 # means there is only the header row...so no hits:
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163 return None
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164
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165 for data_row in data_rows:
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166 if not data_row.strip() == '':
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167 row_as_list = _str_to_list(data_row, delimiter='\t')
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168 result.append(row_as_list)
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169
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170 # return result processed into a dict:
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171 return _process_data(result)
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172
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173 except urllib2.HTTPError, e:
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174 raise Exception( "HTTP error for URL: " + url + " : %s - " % e.code + e.reason)
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175 except urllib2.URLError, e:
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176 raise Exception( "Network error: %s" % e.reason.args[1] + ". Administrator: please check if MetExp service [" + url + "] is accessible from your Galaxy server. ")
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177
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178 def _str_to_list(data_row, delimiter='\t'):
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179 result = []
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180 for column in data_row.split(delimiter):
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181 result.append(column)
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182 return result
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183
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184
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185 # alternative: ?
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186 # s = requests.Session()
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187 # s.verify = False
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188 # #s.auth = (token01, token02)
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189 # resp = s.get(url, params={'name': 'anonymous'}, stream=True)
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190 # content = resp.content
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191 # # transform to dictionary:
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192
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193
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194
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195
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196 def _merge_data(input_data_record, extra_cols):
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197 '''
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198 Adds the extra information to the existing data record and returns
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199 the combined new record.
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200 '''
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201 record = []
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202 for column in input_data_record:
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203 record.append(input_data_record[column])
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204
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205
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206 # add extra columns
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207 for column in extra_cols:
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208 record.append(column)
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209
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210 return record
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211
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212
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213 def _save_data(data_rows, headers, out_csv):
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214 '''
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215 Writes tab-separated data to file
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216 @param data_rows: dictionary containing merged/enriched dataset
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217 @param out_csv: output csv file
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218 '''
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219
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220 # Open output file for writing
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221 outfile_single_handle = open(out_csv, 'wb')
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222 output_single_handle = csv.writer(outfile_single_handle, delimiter="\t")
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223
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224 # Write headers
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225 output_single_handle.writerow(headers)
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226
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227 # Write one line for each row
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228 for data_row in data_rows:
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229 output_single_handle.writerow(data_row)
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230
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231 def _get_metexp_URL(metexp_dblink_file):
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232 '''
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233 Read out and return the URL stored in the given file.
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234 '''
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235 file_input = fileinput.input(metexp_dblink_file)
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236 try:
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237 for line in file_input:
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238 if line[0] != '#':
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239 # just return the first line that is not a comment line:
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240 return line
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241 finally:
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242 file_input.close()
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243
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244
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245 def main():
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246 '''
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247 MetExp Query main function
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248
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249 The input file can be any tabular file, as long as it contains a column for the molecular mass
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250 and one for the formula of the respective identification. These two columns are then
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251 used to query against MetExp Database.
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252 '''
22
cd4f13119afa Small fix in filters part and improvement in query_metexp time logging
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253 seconds_start = int(round(time.time()))
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254
21
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255 input_file = sys.argv[1]
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256 casid_col = sys.argv[2]
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257 formula_col = sys.argv[3]
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258 molecular_mass_col = sys.argv[4]
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259 metexp_dblink_file = sys.argv[5]
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260 separation_method = sys.argv[6]
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261 output_result = sys.argv[7]
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262
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263 # Parse metexp_dblink_file to find the URL to the MetExp service:
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264 metexp_dblink = _get_metexp_URL(metexp_dblink_file)
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265
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266 # Parse tabular input file into dictionary/array:
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267 input_data = _process_file(input_file)
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268
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269 # Query data against MetExp DB :
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270 enriched_data = _query_and_add_data(input_data, casid_col, formula_col, molecular_mass_col, metexp_dblink, separation_method)
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271 headers = input_data.keys() + ['METEXP hits for ','METEXP hits: organisms', 'METEXP hits: tissues',
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272 'METEXP hits: experiments','METEXP hits: user names','METEXP hits: column types', 'METEXP hits: CAS nrs', 'Link to METEXP hits']
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273
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274 _save_data(enriched_data, headers, output_result)
22
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275
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276 seconds_end = int(round(time.time()))
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277 print "Took " + str(seconds_end - seconds_start) + " seconds"
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278
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279
21
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280
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281 if __name__ == '__main__':
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282 main()