gc.py

来自「ncbi源码」· Python 代码 · 共 90 行

#!/usr/bin/python

# $Id: gc.py,v 1000.0 2003/10/31 21:38:33 gouriano Exp $
#
# Author:  Josh Cherry
#
# calculate G+C+S content
# (from gbench)

import sys
import cgi

def gc_content(seq):
   gc_count = 0;
   for base in seq:
      if(base == 'G' or base == 'C' or base == 'S'):
         gc_count = gc_count + 1
   return float(gc_count) / len(seq)

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 "gc.py",
      menu-item "Test scripts/GC content",
      tooltip "G+C+S content by a python script ",
      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']
for loc in locs:
   seq = cgi.parse_qs(loc);
   print seq['short_title'][0], '\t', gc_content(seq['seq'][0])


# ===========================================================================
# $Log: gc.py,v $
# Revision 1000.0  2003/10/31 21:38:33  gouriano
# PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
#
# Revision 1.3  2003/10/29 20:12:05  jcherry
# Reflect new spec for plugin args
#
# Revision 1.2  2003/10/07 19:12:25  jcherry
# Reflected change of PluginURL to PluginValue (changed addr to
# value in asn.1)
#
# Revision 1.1  2003/07/28 18:24:31  jcherry
# Initial version
#
# ===========================================================================
# 
#  ===========================================================================
#  PRODUCTION $Log: gc.py,v $
#  PRODUCTION Revision 1000.0  2003/10/31 21:38:33  gouriano
#  PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.3
#  PRODUCTION
#  ===========================================================================
#