Added script fastaq_to_orfs_gff

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:

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] <fasta/q in> <gff_out>')
+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)