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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import os
import shutil
import sys
if len(sys.argv) != 3:
print ("Converter for genes and operons files from .txt to .gff format")
print ("Usage: " + sys.argv[0] + " <input .txt file> <keyword: either 'gene' or 'operon'>")
sys.exit(1)
input_filename = sys.argv[1]
keyword = sys.argv[2]
if not os.path.exists(input_filename):
print ("Specified file not found! Exiting...")
sys.exit(1)
basename = os.path.splitext(input_filename)[0]
output_filename = basename + ".gff"
if os.path.exists(output_filename):
print ("Output file (" + output_filename + ") already exists! Exiting...")
sys.exit(1)
out = open(output_filename, 'w')
out.write("##gff-version 2\n")
for line in open(input_filename, 'r'):
# EXAMPLE:
# gi|48994873|gb|U00096.2| 1 4263805 4264884
# gi|48994873|gb|U00096.2| 2 795085 795774
sections = line.split()
if len(sections) != 4:
continue
ref_id = sections[0]
gene_id = sections[1]
start = int(sections[2])
end = int(sections[3])
# EXAMPLE:
# ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
out.write(ref_id + '\t' + '.' + '\t' + keyword + '\t')
out.write(str(min(start, end)) + '\t' + str(max(start, end)) + '\t' + '.' + '\t')
if start < end:
out.write('+')
else:
out.write('-')
out.write('\t' + '.' + '\t' + 'ID=' + gene_id + '\n')
out.close()
print ("Conversion finished! See " + output_filename)
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