diff list-chrom-cols.py @ 6:f86fec07f392 draft default tip

planemo upload commit c397cd8a93953798d733fd62653f7098caac30ce

--- a/list-chrom-cols.py	Wed Apr 19 10:00:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-#!/usr/bin/env python
-# vi: fdm=marker
-
-import argparse
-import subprocess
-import re
-import urllib2
-import json
-import csv
-
-# Get chrom cols {{{1
-################################################################
-
-def get_chrom_cols(dbtype, dburl, dbtoken = None, col_field = 'chromcol'):
-    
-    cols = []
-    
-    if dbtype == 'peakforest':
-        url = dburl + ( '' if dburl[-1] == '/' else '/' ) + 'metadata/lc/list-code-columns'
-        if dbtoken is not None:
-            url += '?token=' + dbtoken
-        result = urllib2.urlopen(url).read()
-        v = json.JSONDecoder().decode(result)
-        i = 0
-        for colid, coldesc in v.iteritems():
-            s = coldesc['name'] + ' - ' + coldesc['constructor'] + ' - L' + str(coldesc['length']) + ' - diam. ' + str(coldesc['diameter']) + ' - part. ' + str(coldesc['particule_size']) + ' - flow ' + str(coldesc['flow_rate'])
-            cols.append( (s , colid, i == 0) )
-            ++i
-        
-    elif dbtype == 'inhouse':
-                
-        # Get all column names from file
-        with open(dburl if isinstance(dburl, str) else dburl.get_file_name(), 'r') as dbfile:
-            reader = csv.reader(dbfile, delimiter = "\t", quotechar='"')
-            header = reader.next()
-            if col_field in header:
-                i = header.index(col_field)
-                allcols = []
-                for row in reader:
-                    col = row[i]
-                    if col not in allcols:
-                        allcols.append(col)
-                for i, c in enumerate(allcols):
-                    cols.append( (c, c, i == 0) )
-    
-    return cols
-
-# Main {{{1
-################################################################
-
-if __name__ == '__main__':
-    
-    # Parse command line arguments
-    parser = argparse.ArgumentParser(description='Script for getting chromatographic columns of an RMSDB database for Galaxy tool lcmsmatching.')
-    parser.add_argument('-d', help = 'Database type',       dest = 'dbtype',    required = True)
-    parser.add_argument('-u', help = 'Database URL',        dest = 'dburl',     required = True)
-    parser.add_argument('-t', help = 'Database token',      dest = 'dbtoken',   required = False)
-    parser.add_argument('-f', help = 'Chromatogrphic column field name',     dest = 'col_field',  required = False)
-    args = parser.parse_args()
-    args_dict = vars(args)
-    
-    print(get_chrom_cols(**args_dict))