Mercurial > repos > prog > lcmsmatching

annotate list-chrom-cols.py @ 6:b8f70d8216b3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit b3a4e34cf9356447ae3507cc6fe2ff6a1f24afbc-dirty
author prog
date Mon, 27 Mar 2017 06:27:29 -0400
parents 45e985cd8e9e
children
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1 #!/usr/bin/env python
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2 # vi: fdm=marker
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4 import argparse
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5 import subprocess
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6 import re
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7 import urllib2
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8 import json
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9 import csv
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11 # Get chrom cols {{{1
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12 ################################################################
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14 def get_chrom_cols(dbtype, dburl, dbtoken = None, col_field = 'chromcol'):
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16 cols = []
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18 if dbtype == 'peakforest':
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19 url = dburl + ( '' if dburl[-1] == '/' else '/' ) + 'metadata/lc/list-code-columns'
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20 if dbtoken is not None:
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21 url += '?token=' + dbtoken
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22 result = urllib2.urlopen(url).read()
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23 v = json.JSONDecoder().decode(result)
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24 i = 0
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25 for colid, coldesc in v.iteritems():
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26 s = coldesc['name'] + ' - ' + coldesc['constructor'] + ' - L' + str(coldesc['length']) + ' - diam. ' + str(coldesc['diameter']) + ' - part. ' + str(coldesc['particule_size']) + ' - flow ' + str(coldesc['flow_rate'])
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27 cols.append( (s , colid, i == 0) )
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28 ++i
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30 elif dbtype == 'inhouse':
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32 # Get all column names from file
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33 with open(dburl if isinstance(dburl, str) else dburl.get_file_name(), 'r') as dbfile:
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34 reader = csv.reader(dbfile, delimiter = "\t", quotechar='"')
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35 header = reader.next()
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36 if col_field in header:
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37 i = header.index(col_field)
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38 allcols = []
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39 for row in reader:
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40 col = row[i]
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41 if col not in allcols:
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42 allcols.append(col)
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43 for i, c in enumerate(allcols):
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44 cols.append( (c, c, i == 0) )
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46 return cols
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47
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48 # Main {{{1
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49 ################################################################
1
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51 if __name__ == '__main__':
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52
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53 # Parse command line arguments
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54 parser = argparse.ArgumentParser(description='Script for getting chromatographic columns of an RMSDB database for Galaxy tool lcmsmatching.')
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55 parser.add_argument('-d', help = 'Database type', dest = 'dbtype', required = True)
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56 parser.add_argument('-u', help = 'Database URL', dest = 'dburl', required = True)
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57 parser.add_argument('-t', help = 'Database token', dest = 'dbtoken', required = False)
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58 parser.add_argument('-f', help = 'Chromatogrphic column field name', dest = 'col_field', required = False)
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59 args = parser.parse_args()
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60 args_dict = vars(args)
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61
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62 print(get_chrom_cols(**args_dict))