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

リビジョン 2, 4.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1# converter for ldreduced rgenetics datatype
2# used for grr and eigenstrat - shellfish if we get around to it
3#
4
5import os,sys,tempfile,subprocess,time
6
7from galaxy import eggs
8
9prog="pbed_ldreduced_converter.py"
10
11galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
12<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
13<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
14<head>
15<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
16<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
17<title></title>
18<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
19</head>
20<body>
21<div class="document">
22"""
23
24plinke = 'plink'
25
26
27def timenow():
28    """return current time as a string
29    """
30    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
31
32
33def pruneLD(plinktasks=[],cd='./',vclbase = []):
34    """
35    """
36    fplog,plog = tempfile.mkstemp()
37    alog = []
38    alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
39    for task in plinktasks: # each is a list
40        vcl = vclbase + task
41        sto = file(plog,'w')
42        x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
43        retval = x.wait()
44        sto.close()
45        try:
46            lplog = file(plog,'r').readlines()
47            lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
48            alog += lplog
49            alog.append('\n')
50            os.unlink(plog) # no longer needed
51        except:
52            alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
53    return alog
54 
55
56def makeLDreduced(basename,infpath=None,outfpath=None,plinke='plink',forcerebuild=False,returnFname=False,
57        winsize="60", winmove="40", r2thresh="0.1" ):
58    """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
59    """
60    ldr = basename # we store ld reduced and thinned data
61    ldreduced = os.path.join(outfpath,ldr) # note where this is going
62    outbase = os.path.join(outfpath,basename)
63    inbase = os.path.join(infpath)
64    loglines = []
65    ldbedname = '%s.bed' % ldreduced
66    bedname = '%s.bed' % basename
67    ldbedfn = os.path.join(infpath,ldbedname)
68    bedfn = os.path.join(infpath,bedname)
69    bmap = os.path.join(infpath,'%s.bim' % basename)
70    plinktasks = []
71    vclbase = [plinke,'--noweb']
72    plinktasks += [['--bfile',inbase,'--indep-pairwise %s %s %s' % (winsize,winmove,r2thresh),'--out %s' % outbase],
73            ['--bfile',inbase,'--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
74    vclbase = [plinke,'--noweb']
75    loglines = pruneLD(plinktasks=plinktasks,cd=outfpath,vclbase = vclbase)
76
77def main():
78    """
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">
82   pbed_ldreduced_converter.py '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
83   '$output1' '$output1.files_path' 'plink'   
84  </command>
85    """
86    nparm = 7
87    if len(sys.argv) < nparm:
88        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm))
89        sys.exit(1)
90    inpedfilepath = sys.argv[1]
91    base_name = os.path.split(inpedfilepath)[-1]
92    winsize = sys.argv[2]
93    winmove = sys.argv[3]
94    r2thresh = sys.argv[4]
95    outhtmlname = sys.argv[5]
96    outfilepath = sys.argv[6]
97    try:
98        os.makedirs(outfilepath)
99    except:
100        pass
101    plink = sys.argv[7]
102    makeLDreduced(base_name,infpath=inpedfilepath,outfpath=outfilepath,plinke=plink,forcerebuild=False,returnFname=False,
103        winsize=winsize,winmove=winmove,r2thresh=r2thresh)
104    f = file(outhtmlname,'w')
105    f.write(galhtmlprefix % prog)
106    flist = os.listdir(outfilepath)
107    s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info
108    s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name,winsize,winmove,r2thresh)
109    print '%s %s' % (s1,s2)
110    f.write('<div>%s\n%s\n<ol>' % (s1,s2))
111    for i, data in enumerate( flist ):
112        f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1]))
113    f.write("</div></body></html>")
114    f.close()
115 
116
117if __name__ == "__main__":
118   main()
119
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