prodigal_script.py

#!/usr/bin/env python
import os, subprocess, argparse


# parser = argparse.ArgumentParser(description='Running Prodigal')

# parser.add_argument('-i', '--input_folder',  help='Directory containing input genomes files (.fasta)', type=str)
# parser.add_argument('-f', '--output_format', help='Output Format (gff, gbk, sqn, sco)', default='gff', type=str, nargs='?')
# parser.add_argument('-o', '--output', help='Output foler, default to ./output ', default='output', type=str, nargs='?')
# parser.add_argument('-a', '--proteins', help='fna folder, default to ./proteins', default='proteins', type=str, nargs='?')
# parser.add_argument('-d', '--nucleotides', help='fna folder, default to ./nucleotides ', default='nucleotides', type=str, nargs='?')
# # parser.add_argument('-o', '--output', help='Output file name, default to “./output” if -o is provided with noadditionalstrings. If-oisnotprovided,writetoSTDOUT', const='./output', nargs='?', type=str)
# # parser.add_argument('-t', '--threads', help='Number of theads/processes to run the analysis, defaults to 1', default=1, type=int, nargs='?')
# # parser.add_argument('-v', '--verbose', help='Verbose mode', action='store_true')
# # parser.add_argument('-f', '--force', help='Overwrite files if they exist. Do not overwrite by default', action='store_true')
# args = parser.parse_args()

def run_prodigal(input_folder, output_format='gff', output='output', proteins='proteins', nucleotides='nucleotides'):
	for file in os.listdir(input_folder):
		if os.path.isfile(os.path.join(input_folder, file)):
			input_file = os.path.join(input_folder, file)
			faa = os.path.join(input_folder, proteins, file.split('.')[0])
			#Create Protein Directory if it does not exists
			if not os.path.exists(os.path.join(input_folder, proteins)):
			    os.makedirs(os.path.join(input_folder, proteins))
			fna = os.path.join(input_folder, nucleotides, file.split('.')[0])
			#Create Nucelotide Directory if it does not exists
			if not os.path.exists(os.path.join(input_folder, nucleotides)):
			    os.makedirs(os.path.join(input_folder, nucleotides))
			output = os.path.join(input_folder, output, file.split('.')[0])
			#Create Output Directory if it does not exists
			if not os.path.exists(os.path.join(input_folder, output)):
			    os.makedirs(os.path.join(input_folder, output))
			subprocess.run(['prodigal', '-i', input_file, '-o', output, '-a', faa, '-f', output_format, '-d', fna])
			print ('Processing ' + input_file)