root/galaxy-central/lib/galaxy/datatypes/converters/lped_to_fped_converter.py @ 2

リビジョン 2, 3.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1# for rgenetics - lped to fbat
2# recode to numeric fbat version
3# much slower so best to always
4# use numeric alleles internally
5
6import sys,os,time
7
8
9prog = os.path.split(sys.argv[0])[-1]
10myversion = 'Oct 10 2009'
11
12galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
13<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
14<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
15<head>
16<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
17<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
18<title></title>
19<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
20</head>
21<body>
22<div class="document">
23"""
24
25def timenow():
26    """return current time as a string
27    """
28    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
29
30
31def rgConv(inpedfilepath,outhtmlname,outfilepath):
32  """convert linkage ped/map to fbat""" 
33  recode={'A':'1','C':'2','G':'3','T':'4','N':'0','0':'0','1':'1','2':'2','3':'3','4':'4'}
34  basename = os.path.split(inpedfilepath)[-1] # get basename
35  inmap = '%s.map' % inpedfilepath
36  inped = '%s.ped' % inpedfilepath
37  outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data
38  outfpath = os.path.join(outfilepath,outf) # where to write the fbat format file to
39  try:
40    mf = file(inmap,'r')
41  except:
42    sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog,inmap))
43    sys.exit(1)
44  try:
45    rsl = [x.split()[1] for x in mf]
46  except:
47      sys.stderr.write('## cannot parse %s' % inmap)
48      sys.exit(1)
49  try:
50      os.makedirs(outfilepath)
51  except:
52      pass # already exists
53  head = ' '.join(rsl) # list of rs numbers
54  # TODO add anno to rs but fbat will prolly barf?
55  pedf = file(inped,'r')
56  o = file(outfpath,'w',2**20)
57  o.write(head)
58  o.write('\n')
59  for i,row in enumerate(pedf):
60    if i == 0:
61       lrow = row.split()
62       try:
63          x = [int(x) for x in lrow[10:50]] # look for non numeric codes
64       except:
65          dorecode = 1
66    if dorecode:
67        lrow = row.strip().split()
68        p = lrow[:6]
69        g = lrow[6:]
70        gc = [recode.get(x,'0') for x in g]
71        lrow = p+gc
72        row = '%s\n' % ' '.join(lrow)
73    o.write(row)
74  o.close()
75
76
77def main():
78    """call fbater
79    need to work with rgenetics composite datatypes
80    so in and out are html files with data in extrafiles path
81    <command interpreter="python">rg_convert_lped_fped.py '$input1/$input1.metadata.base_name'
82    '$output1' '$output1.extra_files_path'
83    </command>
84    """
85    nparm = 3
86    if len(sys.argv) < nparm:
87        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
88        sys.exit(1)
89    inpedfilepath = sys.argv[1]
90    outhtmlname = sys.argv[2]
91    outfilepath = sys.argv[3]
92    try:
93        os.makedirs(outfilepath)
94    except:
95        pass
96    rgConv(inpedfilepath,outhtmlname,outfilepath)
97    f = file(outhtmlname,'w')
98    f.write(galhtmlprefix % prog)
99    flist = os.listdir(outfilepath)
100    print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
101    f.write('<div>## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n<ol>' % (prog,timenow()))
102    for i, data in enumerate( flist ):
103        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
104    f.write("</div></body></html>")
105    f.close()
106
107 
108
109if __name__ == "__main__":
110   main()
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