lped_to_fped_converter.py - This is a Python script that co…

/lib/galaxy/datatypes/converters/lped_to_fped_converter.py

https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 110 lines · 87 code · 12 blank · 11 comment · 14 complexity · f00fe3393499259e186fe32fd3db09a0 MD5 · raw file


# for rgenetics - lped to fbat
# recode to numeric fbat version
# much slower so best to always
# use numeric alleles internally

import sys,os,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">
"""

def timenow():
    """return current time as a string
    """
    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))


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 = file(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 = file(inped,'r')
  o = file(outfpath,'w',2**20)
  o.write(head)
  o.write('\n')
  for i,row in enumerate(pedf):
    if i == 0:
       lrow = row.split()
       try:
          x = [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(x,'0') for x in g]
        lrow = p+gc
        row = '%s\n' % ' '.join(lrow)
    o.write(row)
  o.close()


def main():
    """call fbater
    need to work with rgenetics composite datatypes
    so in and out are html files with data in extrafiles path
    <command interpreter="python">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)
    f = file(outhtmlname,'w')
    f.write(galhtmlprefix % prog)
    flist = os.listdir(outfilepath)
    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>")
    f.close()



if __name__ == "__main__":
   main()