# 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">
<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">
"""
[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()