Source code for galaxy.datatypes.converters.lped_to_fped_converter

# 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" "">
<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">

[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 '$__tool_directory__/' '$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: Galaxy Tools {prog} {timenow()}") # becomes info f.write(f"<div>## Rgenetics: 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()