Mercurial > repos > prog > lcmsmatching

comparison list-chrom-cols.py @ 5:fb9c0409d85c draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 608d9e59a0d2dcf85a037968ddb2c61137fb9bce
author prog
date Wed, 19 Apr 2017 10:00:05 -0400
parents 20d69a062da3
children
comparison
equal deleted inserted replaced
4:b34c14151f25 5:fb9c0409d85c
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 # vi: fdm=marker
2 3
3 import argparse 4 import argparse
4 import subprocess 5 import subprocess
5 import re 6 import re
6 import urllib2 7 import urllib2
7 import json 8 import json
8 import csv 9 import csv
9 10
10 def get_chrom_cols(dbtype, dburl, dbtoken = None, dbfields = None): 11 # Get chrom cols {{{1
12 ################################################################
13
14 def get_chrom_cols(dbtype, dburl, dbtoken = None, col_field = 'chromcol'):
11 15
12 cols = [] 16 cols = []
13 17
14 if dbtype == 'peakforest': 18 if dbtype == 'peakforest':
15 url = dburl + ( '' if dburl[-1] == '/' else '/' ) + 'metadata/lc/list-code-columns' 19 url = dburl + ( '' if dburl[-1] == '/' else '/' ) + 'metadata/lc/list-code-columns'
17 url += '?token=' + dbtoken 21 url += '?token=' + dbtoken
18 result = urllib2.urlopen(url).read() 22 result = urllib2.urlopen(url).read()
19 v = json.JSONDecoder().decode(result) 23 v = json.JSONDecoder().decode(result)
20 i = 0 24 i = 0
21 for colid, coldesc in v.iteritems(): 25 for colid, coldesc in v.iteritems():
22 cols.append( (coldesc['name'], colid, i == 0) ) 26 s = coldesc['name'] + ' - ' + coldesc['constructor'] + ' - L' + str(coldesc['length']) + ' - diam. ' + str(coldesc['diameter']) + ' - part. ' + str(coldesc['particule_size']) + ' - flow ' + str(coldesc['flow_rate'])
27 cols.append( (s , colid, i == 0) )
23 ++i 28 ++i
24 29
25 elif dbtype == 'inhouse': 30 elif dbtype == 'inhouse':
26 # Get field for chromatographic column name
27 col_field = 'chromcol'
28 if dbfields is not None:
29 fields = dict(u.split("=") for u in dbfields.split(","))
30 if 'chromcol' in fields:
31 col_field = fields['chromcol']
32 31
33 # Get all column names from file 32 # Get all column names from file
34 with open(dburl if isinstance(dburl, str) else dburl.get_file_name(), 'rb') as dbfile: 33 with open(dburl if isinstance(dburl, str) else dburl.get_file_name(), 'r') as dbfile:
35 reader = csv.reader(dbfile, delimiter = "\t", quotechar='"') 34 reader = csv.reader(dbfile, delimiter = "\t", quotechar='"')
36 header = reader.next() 35 header = reader.next()
37 if col_field in header: 36 if col_field in header:
38 i = header.index(col_field) 37 i = header.index(col_field)
39 allcols = [] 38 allcols = []
44 for i, c in enumerate(allcols): 43 for i, c in enumerate(allcols):
45 cols.append( (c, c, i == 0) ) 44 cols.append( (c, c, i == 0) )
46 45
47 return cols 46 return cols
48 47
49 ######## 48 # Main {{{1
50 # MAIN # 49 ################################################################
51 ########
52 50
53 if __name__ == '__main__': 51 if __name__ == '__main__':
54 52
55 # Parse command line arguments 53 # Parse command line arguments
56 parser = argparse.ArgumentParser(description='Script for getting chromatographic columns of an RMSDB database for Galaxy tool lcmsmatching.') 54 parser = argparse.ArgumentParser(description='Script for getting chromatographic columns of an RMSDB database for Galaxy tool lcmsmatching.')
57 parser.add_argument('-d', help = 'Database type', dest = 'dbtype', required = True) 55 parser.add_argument('-d', help = 'Database type', dest = 'dbtype', required = True)
58 parser.add_argument('-u', help = 'Database URL', dest = 'dburl', required = True) 56 parser.add_argument('-u', help = 'Database URL', dest = 'dburl', required = True)
59 parser.add_argument('-t', help = 'Database token', dest = 'dbtoken', required = False) 57 parser.add_argument('-t', help = 'Database token', dest = 'dbtoken', required = False)
60 parser.add_argument('-f', help = 'Database fields', dest = 'dbfields', required = False) 58 parser.add_argument('-f', help = 'Chromatogrphic column field name', dest = 'col_field', required = False)
61 args = parser.parse_args() 59 args = parser.parse_args()
62 args_dict = vars(args) 60 args_dict = vars(args)
63 61
64 print(get_chrom_cols(**args_dict)) 62 print(get_chrom_cols(**args_dict))