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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

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=None, cd='./', vclbase=None): """ """ plinktasks = plinktasks or [] vclbase = vclbase or [] alog = ['## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n'] with tempfile.NamedTemporaryFile(mode='r+') as plog: for task in plinktasks: # each is a list vcl = vclbase + task subprocess.check_call(vcl, stdout=plog, stderr=plog, cwd=cd) try: plog.seek(0) lplog = [elem for elem in plog.readlines() if elem.find('Pruning SNP') == -1] alog += lplog alog.append('\n') except Exception: alog.append('### {} Strange - no std out from plink when running command line\n{}\n'.format(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, f'--indep-pairwise {winsize} {winmove} {r2thresh}', '--out %s' % outbase], ['--bfile', inbase, f'--extract {outbase}.prune.in --make-bed --out {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 = f'## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}' # becomes info s2 = f'Input {base_name}, winsize={winsize}, winmove={winmove}, r2thresh={r2thresh}' print(f'{s1} {s2}') f.write(f'<div>{s1}\n{s2}\n<ol>') for data in flist: f.write('<li><a href="{}">{}</a></li>\n'.format(os.path.split(data)[-1], os.path.split(data)[-1])) f.write("</div></body></html>")
if __name__ == "__main__": main()