# for rgenetics - lped to fbat
# recode to numeric fbat version
# much slower so best to always
# use numeric alleles internally
import os
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 rgConv(inpedfilepath, outhtmlname, outfilepath):
"""convert linkage ped/map to fbat"""
recode = {"A": "1", "C": "2", "G": "3", "T": "4", "N": "0", "0": "0", "1": "1", "2": "2", "3": "3", "4": "4"}
basename = os.path.split(inpedfilepath)[-1] # get basename
inmap = f"{inpedfilepath}.map"
inped = f"{inpedfilepath}.ped"
outf = f"{basename}.ped" # note the fbat exe insists that this is the extension for the ped data
outfpath = os.path.join(outfilepath, outf) # where to write the fbat format file to
try:
mf = open(inmap)
except Exception:
sys.exit(f"{prog} cannot open inmap file {inmap} - do you have permission?\n")
try:
rsl = [x.split()[1] for x in mf]
except Exception:
sys.exit(f"## cannot parse {inmap}")
try:
os.makedirs(outfilepath)
except Exception:
pass # already exists
head = " ".join(rsl) # list of rs numbers
# TODO add anno to rs but fbat will prolly barf?
with open(inped) as pedf, open(outfpath, "w", 2**20) as o:
o.write(head)
o.write("\n")
for i, row in enumerate(pedf):
if i == 0:
lrow = row.split()
try:
[int(x) for x in lrow[10:50]] # look for non numeric codes
except Exception:
dorecode = 1
if dorecode:
lrow = row.strip().split()
p = lrow[:6]
g = lrow[6:]
gc = [recode.get(z, "0") for z in g]
lrow = p + gc
row = f"{' '.join(lrow)}\n"
o.write(row)
[docs]def main():
"""call fbater
need to work with rgenetics composite datatypes
so in and out are html files with data in extrafiles path
<command>python '$__tool_directory__/rg_convert_lped_fped.py' '$input1/$input1.metadata.base_name'
'$output1' '$output1.extra_files_path'
</command>
"""
nparm = 3
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
rgConv(inpedfilepath, outhtmlname, outfilepath)
flist = os.listdir(outfilepath)
with open(outhtmlname, "w") as f:
f.write(galhtmlprefix % prog)
print(f"## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}") # becomes info
f.write(f"<div>## Rgenetics: http://rgenetics.org Galaxy Tools {prog} {timenow()}\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()