/lib/galaxy/datatypes/converters/lped_to_fped_converter.py
Python | 110 lines | 102 code | 4 blank | 4 comment | 0 complexity | f00fe3393499259e186fe32fd3db09a0 MD5 | raw file
1# for rgenetics - lped to fbat 2# recode to numeric fbat version 3# much slower so best to always 4# use numeric alleles internally 5 6import sys,os,time 7 8 9prog = os.path.split(sys.argv[0])[-1] 10myversion = 'Oct 10 2009' 11 12galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?> 13<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 14<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 15<head> 16<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 17<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org" /> 18<title></title> 19<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 20</head> 21<body> 22<div class="document"> 23""" 24 25def timenow(): 26 """return current time as a string 27 """ 28 return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time())) 29 30 31def rgConv(inpedfilepath,outhtmlname,outfilepath): 32 """convert linkage ped/map to fbat""" 33 recode={'A':'1','C':'2','G':'3','T':'4','N':'0','0':'0','1':'1','2':'2','3':'3','4':'4'} 34 basename = os.path.split(inpedfilepath)[-1] # get basename 35 inmap = '%s.map' % inpedfilepath 36 inped = '%s.ped' % inpedfilepath 37 outf = '%s.ped' % basename # note the fbat exe insists that this is the extension for the ped data 38 outfpath = os.path.join(outfilepath,outf) # where to write the fbat format file to 39 try: 40 mf = file(inmap,'r') 41 except: 42 sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog,inmap)) 43 sys.exit(1) 44 try: 45 rsl = [x.split()[1] for x in mf] 46 except: 47 sys.stderr.write('## cannot parse %s' % inmap) 48 sys.exit(1) 49 try: 50 os.makedirs(outfilepath) 51 except: 52 pass # already exists 53 head = ' '.join(rsl) # list of rs numbers 54 # TODO add anno to rs but fbat will prolly barf? 55 pedf = file(inped,'r') 56 o = file(outfpath,'w',2**20) 57 o.write(head) 58 o.write('\n') 59 for i,row in enumerate(pedf): 60 if i == 0: 61 lrow = row.split() 62 try: 63 x = [int(x) for x in lrow[10:50]] # look for non numeric codes 64 except: 65 dorecode = 1 66 if dorecode: 67 lrow = row.strip().split() 68 p = lrow[:6] 69 g = lrow[6:] 70 gc = [recode.get(x,'0') for x in g] 71 lrow = p+gc 72 row = '%s\n' % ' '.join(lrow) 73 o.write(row) 74 o.close() 75 76 77def main(): 78 """call fbater 79 need to work with rgenetics composite datatypes 80 so in and out are html files with data in extrafiles path 81 <command interpreter="python">rg_convert_lped_fped.py '$input1/$input1.metadata.base_name' 82 '$output1' '$output1.extra_files_path' 83 </command> 84 """ 85 nparm = 3 86 if len(sys.argv) < nparm: 87 sys.stderr.write('## %s called with %s - needs %d parameters \n' % (prog,sys.argv,nparm)) 88 sys.exit(1) 89 inpedfilepath = sys.argv[1] 90 outhtmlname = sys.argv[2] 91 outfilepath = sys.argv[3] 92 try: 93 os.makedirs(outfilepath) 94 except: 95 pass 96 rgConv(inpedfilepath,outhtmlname,outfilepath) 97 f = file(outhtmlname,'w') 98 f.write(galhtmlprefix % prog) 99 flist = os.listdir(outfilepath) 100 print '## Rgenetics: http://rgenetics.org Galaxy Tools %s %s' % (prog,timenow()) # becomes info 101 f.write('<div>## Rgenetics: http://rgenetics.org Galaxy Tools %s %s\n<ol>' % (prog,timenow())) 102 for i, data in enumerate( flist ): 103 f.write('<li><a href="%s">%s</a></li>\n' % (os.path.split(data)[-1],os.path.split(data)[-1])) 104 f.write("</div></body></html>") 105 f.close() 106 107 108 109if __name__ == "__main__": 110 main()