Source code for galaxy.datatypes.converters.pbed_ldreduced_converter

# converter for ldreduced rgenetics datatype
# used for grr and eigenstrat - shellfish if we get around to it
from __future__ import print_function

import os
import subprocess
import sys
import tempfile
import time

prog = "pbed_ldreduced_converter.py"

galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org" />
<title></title>
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body>
<div class="document">
"""

plinke = 'plink'


[docs]def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))


[docs]def pruneLD(plinktasks=[], cd='./', vclbase=[]):
    """
    """
    fplog, plog = tempfile.mkstemp()
    alog = []
    alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
    for task in plinktasks:  # each is a list
        vcl = vclbase + task
        with open(plog, 'w') as sto:
            subprocess.check_call(vcl, stdout=sto, stderr=sto, cwd=cd)
        try:
            lplog = open(plog, 'r').readlines()
            lplog = [elem for elem in lplog if elem.find('Pruning SNP') == -1]
            alog += lplog
            alog.append('\n')
            os.unlink(plog)  # no longer needed
        except Exception:
            alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(), ' '.join(vcl)))
    return alog


[docs]def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcerebuild=False, returnFname=False,
                  winsize="60", winmove="40", r2thresh="0.1"):
    """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time
    """
    outbase = os.path.join(outfpath, basename)
    inbase = os.path.join(infpath)
    plinktasks = []
    vclbase = [plinke, '--noweb']
    plinktasks += [['--bfile', inbase, '--indep-pairwise %s %s %s' % (winsize, winmove, r2thresh), '--out %s' % outbase],
                   ['--bfile', inbase, '--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]]
    vclbase = [plinke, '--noweb']
    pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase)


[docs]def main():
    """
    need to work with rgenetics composite datatypes
    so in and out are html files with data in extrafiles path

    .. raw:: xml

        <command>
            python '$__tool_directory__/pbed_ldreduced_converter.py' '$input1.extra_files_path/$input1.metadata.base_name' '$winsize' '$winmove' '$r2thresh'
            '$output1' '$output1.files_path' 'plink'
        </command>
    """
    nparm = 7
    if len(sys.argv) < nparm:
        sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm))
        sys.exit(1)
    inpedfilepath = sys.argv[1]
    base_name = os.path.split(inpedfilepath)[-1]
    winsize = sys.argv[2]
    winmove = sys.argv[3]
    r2thresh = sys.argv[4]
    outhtmlname = sys.argv[5]
    outfilepath = sys.argv[6]
    try:
        os.makedirs(outfilepath)
    except Exception:
        pass
    plink = sys.argv[7]
    makeLDreduced(base_name, infpath=inpedfilepath, outfpath=outfilepath, plinke=plink, forcerebuild=False, returnFname=False,
                  winsize=winsize, winmove=winmove, r2thresh=r2thresh)
    flist = os.listdir(outfilepath)
    with open(outhtmlname, 'w') as f:
        f.write(galhtmlprefix % prog)
        s1 = '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog, timenow())  # becomes info
        s2 = 'Input %s, winsize=%s, winmove=%s, r2thresh=%s' % (base_name, winsize, winmove, r2thresh)
        print('%s %s' % (s1, s2))
        f.write('<div>%s\n%s\n<ol>' % (s1, s2))
        for i, data in enumerate(flist):
            f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1], os.path.split(data)[-1]))
        f.write("</div></body></html>")


if __name__ == "__main__":
    main()