dotter.py

ncbi源码

#!/usr/bin/python

# $Id: dotter.py,v 1000.1 2003/11/21 21:44:13 gouriano Exp $
#
# Author:  Josh Cherry
#
# launch dotter (from gbench) using sequences we're handed

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 "dotter.py",
      menu-item "Alignments/Dot matrix comparison",
      tooltip "Dot matrix comparison of sequences using dotter",
      commands algo {
        {
          command 3,
          args {
            {
              name "hseq",
              desc "Horizontal sequence",
              data single object {
                docaddr "(nil)",
                objaddr "(nil)",
                subtype "Seq-loc"
              }
            },
            {
              name "vseq",
              desc "Vertical sequence",
              data single object {
                docaddr "(nil)",
                objaddr "(nil)",
                subtype "Seq-loc"
              }
            }
          }
        }
      }
    }
    '''
   sys.exit(0)

# otherwise, run

hseq = args['hseq'][0]
vseq = args['vseq'][0]

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

# run dotter in background
# redirect all output to /dev/null (otherwise interpreter goes zombie)
os.system('dotter %s %s >& /dev/null &' % (fname0, fname1))

# cheesy: wait a few seconds so dotter can read its files,
# then delete them
import time
time.sleep(5)
os.system('rm %s %s' % (fname0, fname1))


# ===========================================================================
# $Log: dotter.py,v $
# Revision 1000.1  2003/11/21 21:44:13  gouriano
# PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.4
#
# Revision 1.4  2003/11/17 21:55:40  jcherry
# Ask for two single Seq-locs rather than one array
#
# Revision 1.3  2003/10/29 20:12:05  jcherry
# Reflect new spec for plugin args
#
# Revision 1.2  2003/10/07 13:47:02  dicuccio
# Renamed CPluginURL* to CPluginValue*
#
# Revision 1.1  2003/07/28 18:24:31  jcherry
# Initial version
#
# ===========================================================================
# 
#  ===========================================================================
#  PRODUCTION $Log: dotter.py,v $
#  PRODUCTION Revision 1000.1  2003/11/21 21:44:13  gouriano
#  PRODUCTION PRODUCTION: UPGRADED [ORIGINAL] Dev-tree R1.4
#  PRODUCTION
#  ===========================================================================
#