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Source code for galaxy.datatypes.converters.lped_to_pbed_converter

# for rgenetics - lped to pbed
# where to stop with converters
# pbed might be central
# eg lped/eigen/fbat/snpmatrix all to pbed
# and pbed to lped/eigen/fbat/snpmatrix ?
# that's a lot of converters

import os
import subprocess
import sys
import time

prog = os.path.split(sys.argv[0])[-1]
myversion = "Oct 10 2009"

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">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org" />
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
<div class="document">

[docs]def timenow(): """return current time as a string""" return time.strftime("%d/%m/%Y %H:%M:%S", time.localtime(time.time()))
[docs]def getMissval(inped=""): """ read some lines...ugly hack - try to guess missing value should be N or 0 but might be . or - """ commonmissvals = {"N": "N", "0": "0", "n": "n", "9": "9", "-": "-", ".": "."} try: f = open(inped) except Exception: return None # signal no in file missval = None while missval is None: # doggedly continue until we solve the mystery try: line = f.readline() except Exception: break ll = line.split()[6:] # ignore pedigree stuff for c in ll: if commonmissvals.get(c, None): missval = c f.close() return missval if not missval: missval = "N" # punt f.close() return missval
[docs]def rgConv(inpedfilepath, outhtmlname, outfilepath, plink): """ """ pedf = f"{inpedfilepath}.ped" basename = os.path.split(inpedfilepath)[-1] # get basename outroot = os.path.join(outfilepath, basename) missval = getMissval(inped=pedf) if not missval: print(f"### lped_to_pbed_converter.py cannot identify missing value in {pedf}") missval = "0" subprocess.check_call( [plink, "--noweb", "--file", inpedfilepath, "--make-bed", "--out", outroot, "--missing-genotype", missval], cwd=outfilepath, )
[docs]def main(): """ need to work with rgenetics composite datatypes so in and out are html files with data in extrafiles path <command>python '$__tool_directory__/lped_to_pbed_converter.py' '$input1/$input1.metadata.base_name' '$output1' '$output1.extra_files_path' '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' </command> """ nparm = 4 if len(sys.argv) < nparm: sys.exit("## %s called with %s - needs %d parameters \n" % (prog, sys.argv, nparm)) inpedfilepath = sys.argv[1] outhtmlname = sys.argv[2] outfilepath = sys.argv[3] try: os.makedirs(outfilepath) except Exception: pass plink = sys.argv[4] rgConv(inpedfilepath, outhtmlname, outfilepath, plink) flist = os.listdir(outfilepath) with open(outhtmlname, "w") as f: f.write(galhtmlprefix % prog) s = f"## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}" # becomes info print(s) f.write(f"<div>{s}\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("</ol></div></div></body></html>")
if __name__ == "__main__": main()