root/galaxy-central/tools/rgenetics/rgRegion_code.py

リビジョン 2, 1.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1from galaxy import app
2import galaxy.util,string
3
4librepos = '/usr/local/galaxy/data/rg'
5myrepos = '/home/rerla/galaxy'
6marchinirepos = '/usr/local/galaxy/data/rg/snptest'
7
8#Provides Upload tool with access to list of available builds
9
10
11def get_rgRegionOutFormats():
12    """return options for formats"""
13    dat = [['ucsc track','wig',False],['Strict genome graphs (rs+floats)','gg',True],['tab delimited','xls',False]]
14    dat = [(x[0],x[1],x[2]) for x in dat]
15    return dat
16
17
18def get_phecols(phef):
19   """return column names """
20   head = open(phef,'r').next()
21   c = head.strip().split()
22   res = [(cname,cname,False) for cname in c]
23   x,y,z = res[2] # 0,1 = fid,iid
24   res[2] = (x,y,True) # set second selected
25   return res
26
27
28def getAllcols(fname="/usr/local/galaxy/data/camp2007/camp2007.xls",outformat='gg'):
29   """return column names other than chr offset as a select list"""
30   head = open(fname,'r').next()
31   c = head.strip().split()
32   res = [(cname,'%d' % n,True) for n,cname in enumerate(c)]
33 
34   return res
35
36
37def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
38    """Sets the name of the data"""
39    data_name = param_dict.get( 'tag', 'My region' )
40    outformat = param_dict.get( 'outformat', 'gg' )
41    outfile = param_dict.get( 'outfile1', 'lped' )
42    for name, data in out_data.items():
43       if name == 'tag':
44         data = app.datatypes_registry.change_datatype(data, outformat)
45         data.name = data_name
46         out_data[name] = data
47
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