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 = ""

galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "">
<html xmlns="" xml:lang="en" lang="en">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see" />
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
<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: Galaxy Tools 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: lplog = [elem for elem in plog.readlines() if elem.find("Pruning SNP") == -1] alog += lplog alog.append("\n") except Exception: alog.append( f"### {timenow()} Strange - no std out from plink when running command line\n{' '.join(vcl)}\n" ) 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}", f"--out {outbase}"], ["--bfile", inbase, f"--extract {outbase} --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 '$__tool_directory__/' '$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: 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(f'<li><a href="{os.path.split(data)[-1]}">{os.path.split(data)[-1]}</a></li>\n') f.write("</div></body></html>")
if __name__ == "__main__": main()