From 216b2f840787ab4b283b90fa6c32a2b11b34cdfd Mon Sep 17 00:00:00 2001
From: proost <proost@mpimp-golm.mpg.de>
Date: Wed, 3 May 2017 14:41:23 +0200
Subject: [PATCH] bug fix in fasta_to_gtf.py

---
 helper/fasta_to_gtf.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/helper/fasta_to_gtf.py b/helper/fasta_to_gtf.py
index 9e8296a..9e8a261 100644
--- a/helper/fasta_to_gtf.py
+++ b/helper/fasta_to_gtf.py
@@ -4,7 +4,9 @@
 
 fasta_file = sys.argv[1]
 
-fasta_data = Fasta.readfile(fasta_file)
+fh = Fasta()
 
-for k, s in fasta_data.sequences.items():
-    print('%s\t.\tCDS\t1\t%d\t.\t.\t.\tgene_id "Parent=%s"\n' % (k, len(s), k))
+fh.readfile(fasta_file)
+
+for k, s in fh.sequences.items():
+    print('%s\t.\tCDS\t1\t%d\t.\t.\t.\tParent=%s' % (k, len(s), k))