bl2seq.py

来自「ncbi源码」· Python 代码 · 共 59 行

#!/usr/bin/python

# $Id: bl2seq.py,v 1000.0 2003/10/31 21:37:15 gouriano Exp $
#
# Author:  Josh Cherry
#
# align two nucleotide sequences using bl2seq
# (from gbench)

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) != 2:
   sys.stderr.write("need exactly 2 sequences; you supplied %d\n" % len(l))
   sys.exit(1)

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

# run bl2seq, which must be on path
os.system('bl2seq -p blastn -i seq1.fasta -j seq2.fasta')

# then delete temporary fasta files
os.system('rm seq1.fasta seq2.fasta')


# ===========================================================================
# $Log: bl2seq.py,v $
# Revision 1000.0  2003/10/31 21:37:15  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: bl2seq.py,v $
#  PRODUCTION Revision 1000.0  2003/10/31 21:37:15  gouriano
#  PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.1
#  PRODUCTION
#  ===========================================================================
#