From 797305782c32bebbc4f348ef36b8d3abbeac990e Mon Sep 17 00:00:00 2001 From: martinghunt Date: Tue, 8 Apr 2014 08:49:21 +0100 Subject: [PATCH] Added script fastaq_to_orfs_gff --- fastaq/tasks.py | 1 - scripts/fastaq_to_orfs_gff | 13 +++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100755 scripts/fastaq_to_orfs_gff diff --git a/fastaq/tasks.py b/fastaq/tasks.py index c5d50ca..90d3f68 100644 --- a/fastaq/tasks.py +++ b/fastaq/tasks.py @@ -194,7 +194,6 @@ def fastaq_to_orfs_gff(infile, outfile, min_length=300): seq_reader = sequences.file_reader(infile) fout = utils.open_file_write(outfile) for seq in seq_reader: - print(seq.id) orfs = seq.all_orfs(min_length=min_length) for coords, revcomp in orfs: if revcomp: diff --git a/scripts/fastaq_to_orfs_gff b/scripts/fastaq_to_orfs_gff new file mode 100755 index 0000000..0098023 --- /dev/null +++ b/scripts/fastaq_to_orfs_gff @@ -0,0 +1,13 @@ +#!/usr/bin/env python3 + +import argparse +from fastaq import tasks + +parser = argparse.ArgumentParser( + description = 'Writes a GFF file of open reading frames from a fasta/q file', + usage = '%(prog)s [options] ') +parser.add_argument('--min_length', type=int, help='Minimum length of ORF, in nucleotides [%(default)s]', default=300, metavar='INT') +parser.add_argument('infile', help='Name of input fasta/q file') +parser.add_argument('gff_out', help='Name of output gff file') +options = parser.parse_args() +tasks.fastaq_to_orfs_gff(options.infile, options.gff_out, min_length=options.min_length)