bl2seq.py

ncbi源码

#!/usr/bin/python

# $Id: bl2seq.py,v 1000.0 2003/10/31 21:37:46 gouriano Exp $
#
# Author:  Josh Cherry
#
# align two nucleotide sequences using bl2seq
# (from gbench)

import sys
import cgi
import os
import tempfile

def writefasta(seq, fname, seqname):
   s = ">" + seqname + "\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()
args = cgi.parse_qs(input)
action = args['action'][0]

# if a get info call ...
if action == 'info':
   print '''
   PluginInfo ::= {
      ver-major 0,
      ver-minor 0,
      ver-revision 0,
      ver-build-date "",
      class-name "bl2seq.py",
      menu-item "Alignments/Align two sequences using blast",
      tooltip "Align two sequences using blast (bl2seq)",
      commands algo {
        {
          command 3,
          args {
            {
              name "locs",
              desc "Locations to evaluate",
              data array {
                object {
                  docaddr "(nil)",
                  objaddr "(nil)",
                  subtype "Seq-loc"
                }
              }
            }
          }
        }
      }
    }
    '''
   sys.exit(0)

# otherwise, run

locs = args['locs']
if len(locs) != 2:
   sys.stderr.write("need exactly 2 sequences; you supplied %d\n" % len(locs))
   sys.exit(1)

# write temporary fasta files contining the sequences
fname0 = tempfile.mktemp('.fasta')
fname1 = tempfile.mktemp('.fasta')
loc0 = cgi.parse_qs(locs[0]);
loc1 = cgi.parse_qs(locs[1]);
writefasta(loc0['seq'][0], fname0, loc0['title'][0])
writefasta(loc1['seq'][0], fname1, loc1['title'][0])

# run bl2seq, which must be on path
os.system('bl2seq -p blastn -i %s -j %s' % (fname0, fname1))

# then delete temporary fasta files
os.system('rm %s %s' % (fname0, fname1))

# ===========================================================================
# $Log: bl2seq.py,v $
# Revision 1000.0  2003/10/31 21:37:46  gouriano
# PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.4
#
# Revision 1.4  2003/10/29 20:12:05  jcherry
# Reflect new spec for plugin args
#
# Revision 1.3  2003/10/07 19:12:25  jcherry
# Reflected change of PluginURL to PluginValue (changed addr to
# value in asn.1)
#
# Revision 1.2  2003/10/07 13:47:01  dicuccio
# Renamed CPluginURL* to CPluginValue*
#
# Revision 1.1  2003/07/28 18:24:31  jcherry
# Initial version
#
# ===========================================================================
# 
#  ===========================================================================
#  PRODUCTION $Log: bl2seq.py,v $
#  PRODUCTION Revision 1000.0  2003/10/31 21:37:46  gouriano
#  PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.4
#  PRODUCTION
#  ===========================================================================
#