root/galaxy-central/lib/galaxy/datatypes/converters/lped_to_pbed_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 pbed
2# where to stop with converters
3# pbed might be central
4# eg lped/eigen/fbat/snpmatrix all to pbed
5# and pbed to lped/eigen/fbat/snpmatrix ?
6# that's a lot of converters
7import sys,os,time,subprocess
8
9
10prog = os.path.split(sys.argv[0])[-1]
11myversion = 'Oct 10 2009'
12
13galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
14<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
15<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
16<head>
17<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
18<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
19<title></title>
20<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
21</head>
22<body>
23<div class="document">
24"""
25
26def timenow():
27    """return current time as a string
28    """
29    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
30
31def getMissval(inped=''):
32   """
33   read some lines...ugly hack - try to guess missing value
34   should be N or 0 but might be . or -
35   """
36   commonmissvals = {'N':'N','0':'0','n':'n','9':'9','-':'-','.':'.'}
37   try:
38       f = file(inped,'r')
39   except:
40       return None # signal no in file
41   missval = None
42   while missval == None: # doggedly continue until we solve the mystery
43        try:
44          l = f.readline()
45        except:
46          break
47        ll = l.split()[6:] # ignore pedigree stuff
48        for c in ll:
49            if commonmissvals.get(c,None):
50               missval = c
51               f.close()
52               return missval
53   if not missval:
54       missval = 'N' # punt
55   close(f)
56   return missval
57   
58def rgConv(inpedfilepath,outhtmlname,outfilepath,plink):
59    """
60    """
61    pedf = '%s.ped' % inpedfilepath
62    basename = os.path.split(inpedfilepath)[-1] # get basename
63    outroot = os.path.join(outfilepath,basename)
64    missval = getMissval(inped = pedf)
65    if not missval:
66        print '### lped_to_pbed_converter.py cannot identify missing value in %s' % pedf
67        missval = '0'
68    cl = '%s --noweb --file %s --make-bed --out %s --missing-genotype %s' % (plink,inpedfilepath,outroot,missval)
69    p = subprocess.Popen(cl,shell=True,cwd=outfilepath)
70    retval = p.wait() # run plink
71
72
73
74
75def main():
76    """
77    need to work with rgenetics composite datatypes
78    so in and out are html files with data in extrafiles path
79    <command interpreter="python">lped_to_pbed_converter.py '$input1/$input1.metadata.base_name'
80    '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
81    </command>
82    """
83    nparm = 4
84    if len(sys.argv) < nparm:
85        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
86        sys.exit(1)
87    inpedfilepath = sys.argv[1]
88    outhtmlname = sys.argv[2]
89    outfilepath = sys.argv[3]
90    try:
91        os.makedirs(outfilepath)
92    except:
93        pass
94    plink = sys.argv[4]
95    rgConv(inpedfilepath,outhtmlname,outfilepath,plink)
96    f = file(outhtmlname,'w')
97    f.write(galhtmlprefix % prog)
98    flist = os.listdir(outfilepath)
99    s = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
100    print s
101    f.write('<div>%s\n<ol>' % (s))
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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