Mercurial > repos > prog > lcmsmatching

annotate list-ms-mode-values.py @ 7:882f2f20028b draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Sun, 09 Apr 2017 10:44:21 -0400
parents b8f70d8216b3
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1 #!/usr/bin/env python
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2 # vi: fdm=marker
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4 import csv
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5 import re
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6 import argparse
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8 # Get MS mode values {{{1
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9 ################################################################
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11 def get_ms_mode_value(file, col, preferred):
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12
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13 modes = []
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14 cols = []
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15 preferred = preferred.split(',')
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17 with open(file if isinstance(file, str) else file.get_file_name(), 'r') as f:
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19 # Read file header
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20 reader = csv.reader(f, delimiter = "\t", quotechar='"')
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21 header = reader.next()
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22 try:
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23 index = header.index(col)
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24 for row in reader:
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25 v = row[index]
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26 if v not in modes:
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27 modes.append(v)
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28
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29 # Find default value
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30 default = 0
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31 for p in preferred:
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32 for i, m in enumerate(modes):
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33 if m == p:
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34 default = i
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35 break
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36 if default != 0:
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37 break
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39 # Build list of cols
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40 for i, c in enumerate(modes):
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41 cols.append( (c, c, i == default) )
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42 except:
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43 pass
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44
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45 return cols
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47 # Main {{{1
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48 ################################################################
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49
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50 if __name__ == '__main__':
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51
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52 # Parse command line arguments
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53 parser = argparse.ArgumentParser(description='Script for getting column names in a csv file.')
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54 parser.add_argument('-f', help = 'CSV File (separator must be TAB)', dest = 'file', required = True)
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55 parser.add_argument('-c', help = 'MS mode column name.', dest = 'col', required = True)
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56 parser.add_argument('-p', help = 'List (comma separated values) of preferred column names for default one.', dest = 'preferred', required = True)
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57 args = parser.parse_args()
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58 args_dict = vars(args)
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59
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60 print(get_ms_mode_value(**args_dict))