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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
from __future__ import print_function

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 = '%s.map' % inpedfilepath inped = '%s.ped' % inpedfilepath outf = '%s.ped' % basename # 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, 'r') except: sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap)) sys.exit(1) try: rsl = [x.split()[1] for x in mf] except: sys.stderr.write('## cannot parse %s' % inmap) sys.exit(1) try: os.makedirs(outfilepath) except: pass # already exists head = ' '.join(rsl) # list of rs numbers # TODO add anno to rs but fbat will prolly barf? pedf = open(inped, 'r') o = open(outfpath, 'w', 2 ** 20) 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: 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 = '%s\n' % ' '.join(lrow) o.write(row) o.close()
[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.stderr.write('## %s called with %s - needs %d parameters \n' % (prog, sys.argv, nparm)) sys.exit(1) inpedfilepath = sys.argv[1] outhtmlname = sys.argv[2] outfilepath = sys.argv[3] try: os.makedirs(outfilepath) except: pass rgConv(inpedfilepath, outhtmlname, outfilepath) flist = os.listdir(outfilepath) with open(outhtmlname, 'w') as f: f.write(galhtmlprefix % prog) print('## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog, timenow())) # becomes info f.write('<div>## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n<ol>' % (prog, timenow())) for i, data in enumerate(flist): f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1], os.path.split(data)[-1])) f.write("</div></body></html>")
if __name__ == "__main__": main()