RunProkka.ipy

#!/usr/bin/ipython
; -*- mode: python -*- 

import sys
import os

# This script runs the annotations program Prokka on a directory of fasta format
# genomes. Each genome will hava a directory as output. Additionally, a
# directory containing protein sequences in fasta format for each genome will be
# created as well as a directory containing the corresponding nucleotide seqs.

def usage():
    print "RunProkka.ipy\n \
        <directory with fasta genomes>"

if len(sys.argv) != 2:
    usage()
genomeDirectory = sys.argv[1]

# make directories for protein and dna sequences if they don't already exist
!mkdir -p dnaSeqs
!mkdir -p proteinSeqs

# run prokka for each genome in directory

genomes = !ls {genomeDirectory}
for genome in genomes:
    prefix = os.path.splitext(genome)[0]
    print prefix
    outdir = genomeDirectory + prefix + '_annotation'
    print outdir
    !prokka --outdir {outdir} --prefix {prefix} --locustag {prefix} {genomeDirectory + genome}
    !cp {outdir + '/' + prefix + '.faa'} proteinSeqs
    !cp {outdir + '/' + prefix + '.ffn'} dnaSeqs