#!/usr/bin/env python

import os
import os.path
import subprocess
import sys

# SEARCH - a c-shell script 
# SEARCH searches GenBank using fasta
# $1 is a FILESET containing the DNA sequence to search for
# $2 is a FILESET containing the GenBank divisions (3-letter code)
#    you wish to be searched.

testseq = os.path.splitext(sys.argv[1])[0]
file_h  = open(sys.argv[2], 'r')
div     = file_h.readlines()
file_h.close()

if os.environ.has_key('GB'):
    GB = os.environ.get('GB')
if os.environ.has_key('THREADED'):
    THREADED = os.environ.get('THREADED')
os.nice(10)

for line in div:
    for token in line.split():
        if os.path.exists(os.path.join(GB, 'gb' + token + '.ind')):
            NAMESET = (token)
        else:
            index = 1
            NAMESET = ()
            while os.path.exists(os.path.join(GB, 'gb' + token + str(index) + '.wrp')):
                NAMESET.append(token + str(index))
                index += 1
        for name in NAMESET:
            subprocess.call(['fasta3' + THREADED, sys.argv[1], os.path.join(GB, 'gb' + name + '.wrp'), \
                '-k', '-o3', '-Q'], stdout=open(testseq + '.' + name + '.fasta', 'w'))
os.nice(0)