dotter.py

来自「ncbi源码」· Python 代码 · 共 66 行

#!/usr/bin/python

# $Id: dotter.py,v 1000.0 2003/10/31 21:37:23 gouriano Exp $
#
# Author:  Josh Cherry
#
# launch dotter (from gbench) using sequences we're handed

import sys
import string
import commands
import os

def writefasta(seq, fname):
   s = ">" + fname + "\n"
   for pos in range(0, len(seq), 60):
      s += seq[pos:pos+60]
      s += '\n'
   f = open(fname, "w")
   f.write(s)
   f.close

input = sys.stdin.read()
l = string.split(input)
if len(l) != 1 and len(l) != 2:
   sys.stderr.write("need exactly 1 or 2 sequences; you supplied %d\n" % len(l))
   sys.exit(1)
# if given just one sequence, 'double' it to plot against itself
if len(l) == 1:
   l = [ l[0], l[0] ]

writefasta(l[0], 'seq1.fasta')
writefasta(l[1], 'seq2.fasta')

# run dotter in background
# redirect all output to /dev/null (otherwise interpreter goes zombie)
os.system('dotter seq1.fasta seq2.fasta >& /dev/null &')

# cheesey: wait a few seconds so dotter can read its files,
# then delete them
import time
time.sleep(5)
os.system('rm seq1.fasta seq2.fasta')


# ===========================================================================
# $Log: dotter.py,v $
# Revision 1000.0  2003/10/31 21:37:23  gouriano
# PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.1
#
# Revision 1.1  2003/06/24 16:41:12  jcherry
# Initial versions of scripts for use with gbench
#
# ===========================================================================


# 
#  ===========================================================================
#  PRODUCTION $Log: dotter.py,v $
#  PRODUCTION Revision 1000.0  2003/10/31 21:37:23  gouriano
#  PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.1
#  PRODUCTION
#  ===========================================================================
#