#! /usr/bin/env python

# run.py
# P.Clote

import sys,os

def main(filename):
  file = open(filename)
  line = file.readline()
  FASTA = line.strip()
  assert(FASTA[0]=='>')
  pos   = FASTA.find('>')
  FASTA = FASTA[pos+1:].split()[0]
#  pos   = FASTA.find('random')
  pos   = FASTA.find('_')
  DIR   = FASTA[:pos]
  outdirname  = '%s' % DIR
  os.mkdir(outdirname)
  os.chdir(outdirname)
  print os.getcwd()
  while line:
    FASTA = line.strip()
    assert(FASTA[0]=='>')
    pos   = FASTA.find('>')
    FASTA = FASTA[pos+1:].split()[0]
    pos   = FASTA.find('random')
    DIR   = FASTA[:pos-1]
    seq = file.readline().strip()
    text = """#!/bin/csh
#%s
#PBS -q normal
#PBS -l pcput=00:30:00
#PBS -l nodes=1:clotelab

cd $PBS_O_WORKDIR
/usr/local/bin/HPstruct -seq=%s -lat=FCC -maxSol=1 -dbPath=/cluster/data/CPSP_CoreDB"""
    text = text % (FASTA,seq)
    outfilename = '%s.out' % FASTA
    outfile = open(outfilename,'w')
    outfile.write("%s\n" % text)
    outfile.close()
    cmd = "qsub %s" % outfilename
    print cmd
    os.system(cmd)
    line = file.readline()
  file.close()
  os.chdir('..')

if __name__ == '__main__':
  if len(sys.argv) < 2:
    print "%s filename" % sys.argv[0]
    sys.exit(1)
  filename = sys.argv[1]
  main(filename)