annotate export_to_metexp_tabular.py @ 9:0c629990350c

fix

#!/usr/bin/env python
# encoding: utf-8
'''
Module to combine output from the GCMS Galaxy tools RankFilter, CasLookup and MsClust
into a tabular file that can be uploaded to the MetExp database.

RankFilter, CasLookup are already combined by combine_output.py so here we will use
this result. Furthermore here the MsClust spectra file (.MSP) and one of the MsClust
quantification files are to be combined with combine_output.py result as well. 

Extra calculations performed:
- The column MW is also added here and is derived from the column FORMULA found 
  in combine_output.py result. 
  
So in total here we merge 3 files and calculate one new column. 
'''

import csv
import sys
from collections import OrderedDict

__author__ = "Pieter Lukasse"
__contact__ = "[e-mail]"
__copyright__ = "Copyright, 2013, Plant Research International, WUR"
__license__ = "Apache v2"

def _process_data(in_csv, delim='\t'):
    '''
    Generic method to parse a tab-separated file returning a dictionary with named columns
    @param in_csv: input filename to be parsed
    '''
    data = list(csv.reader(open(in_csv, 'rU'), delimiter=delim))
    header = data.pop(0)
    # Create dictionary with column name as key
    output = OrderedDict()
    for index in xrange(len(header)):
        output[header[index]] = [row[index] for row in data]
    return output

ONE_TO_ONE = 'one_to_one'
N_TO_ONE = 'n_to_one'

def _merge_data(set1, link_field_set1, set2, link_field_set2, compare_function, merge_function, relation_type=ONE_TO_ONE):
    '''
    Merges data from both input dictionaries based on the link fields. This method will
    build up a new list containing the merged hits as the items. 
    @param set1: dictionary holding set1 in the form of N lists (one list per attribute name)
    @param set2: dictionary holding set2 in the form of N lists (one list per attribute name)
    '''
    # TODO test for correct input files -> same link_field values should be there (test at least number of unique link_field values):
    #
    # if (len(set1[link_field_set1]) != len(set2[link_field_set2])):
    #    raise Exception('input files should have the same nr of key values  ')
    
    
    merged = []
    processed = {}
    for link_field_set1_idx in xrange(len(set1[link_field_set1])):
        link_field_set1_value = set1[link_field_set1][link_field_set1_idx]
        if not link_field_set1_value in processed :
            # keep track of processed items to not repeat them
            processed[link_field_set1_value] = link_field_set1_value

            # Get the indices for current link_field_set1_value in both data-structures for proper matching
            set1index = [index for index, value in enumerate(set1[link_field_set1]) if value == link_field_set1_value]
            set2index = [index for index, value in enumerate(set2[link_field_set2]) if compare_function(value, link_field_set1_value)==True ]
            
            
            
            merged_hits = []
            # Combine hits
            for hit in xrange(len(set1index)):
                # Create records of hits to be merged ("keys" are the attribute names, so what the lines below do 
                # is create a new "dict" item with same "keys"/attributes, with each attribute filled with its
                # corresponding value in the rankfilter or caslookup tables; i.e. 
                # rankfilter[key] => returns the list/array with size = nrrows, with the values for the attribute
                #                    represented by "key". rindex[hit] => points to the row nr=hit (hit is a rownr/index)
                # It just ensures the entry is made available as a plain named array for easy access.
                rf_record = OrderedDict(zip(set1.keys(), [set1[key][set1index[hit]] for key in set1.keys()]))
                if relation_type == ONE_TO_ONE :
                    cl_record = OrderedDict(zip(set2.keys(), [set2[key][set2index[hit]] for key in set2.keys()]))
                else:
                    # is N to 1:
                    cl_record = OrderedDict(zip(set2.keys(), [set2[key][set2index[0]] for key in set2.keys()]))
                
                merged_hit = merge_function(rf_record, cl_record)
                merged_hits.append(merged_hit)
                
            merged.append(merged_hits)

    return merged, len(set1index)


def _compare_records(key1, key2):
    '''
    in this case the compare method is really simple as both keys are expected to contain 
    same value when records are the same
    '''
    if key1 == key2:
        return True
    else:
        return False
    
    
    
def _merge_records(rank_caslookup_combi, msclust_quant_record):
    '''
    Combines single records from both the RankFilter+CasLookup combi file and from MsClust file
    
    @param rank_caslookup_combi: rankfilter and caslookup combined record (see combine_output.py)
    @param msclust_quant_record: msclust quantification + spectrum record
    '''
    i = 0
    record = []
    for column in rank_caslookup_combi:
        record.append(rank_caslookup_combi[column])
        i += 1
    
    for column in msclust_quant_record:
        record.append(msclust_quant_record[column])
        i += 1
        
    return record




def _save_data(data, headers, nhits, out_csv):
    '''
    Writes tab-separated data to file
    @param data: dictionary containing merged dataset
    @param out_csv: output csv file
    '''

    # Open output file for writing
    outfile_single_handle = open(out_csv, 'wb')
    output_single_handle = csv.writer(outfile_single_handle, delimiter="\t")

    # Write headers
    output_single_handle.writerow(headers)

    # Write one line for each centrotype
    for centrotype_idx in xrange(len(data)):
        for hit in data[centrotype_idx]:
            output_single_handle.writerow(hit)


def main():
    '''
    Combine Output main function
    
    RankFilter, CasLookup are already combined by combine_output.py so here we will use
    this result. Furthermore here the MsClust spectra file (.MSP) and one of the MsClust
    quantification files are to be combined with combine_output.py result as well. 
    '''
    rankfilter_and_caslookup_combined_file = sys.argv[1]
    msclust_quantification_and_spectra_file = sys.argv[2]
    output_csv = sys.argv[3]

    # Read RankFilter and CasLookup output files
    rankfilter_and_caslookup_combined = _process_data(rankfilter_and_caslookup_combined_file)
    msclust_quantification_and_spectra = _process_data(msclust_quantification_and_spectra_file, ',')
    
    merged, nhits = _merge_data(rankfilter_and_caslookup_combined, 'Centrotype', 
                                msclust_quantification_and_spectra, 'centrotype', _compare_records, _merge_records, N_TO_ONE)
    headers = rankfilter_and_caslookup_combined.keys() + msclust_quantification_and_spectra.keys()
    _save_data(merged, headers, nhits, output_csv)


if __name__ == '__main__':
    main()