[med-svn] [qcumber] 04/06: New upstream version 1.0.10+dfsg

[Andreas Tille]

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tille pushed a commit to branch master
in repository qcumber.

commit 3bfb2d96e8a03e48491ff75050caed5914477ab4
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 13 15:14:19 2017 +0100

    New upstream version 1.0.10+dfsg
---
 QCumber.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/QCumber.py b/QCumber.py
index c7eccde..fe7cfdb 100755
--- a/QCumber.py
+++ b/QCumber.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 __author__ = 'LieuV'
-__version__ = "1.0.9"
+__version__ = "1.0.10"
 
 from classes import *
 from helper import *
@@ -233,6 +233,20 @@ def check_input_validity():
 		else:
 			if not os.path.exists(arguments["reference"]):
 				sys.exit("Reference does not exist.")
+			try:
+				from Bio import SeqIO
+				seq_record = SeqIO.parse(arguments["reference"], "fasta")
+			except:
+				print("Couldnt check if reference input is a valid fasta due to missing python library Bio.")
+			try:
+				for seq in seq_record:
+					break  # break after first sequence
+			except FileNotFoundError as err:
+				sys.exit("File %s does not exist" % arguments["reference"])
+			try:
+				str(seq)  # we somehow need to touch the sequence element to trigger an error or not
+			except:
+				sys.exit('File %s does not contain valid fasta data' % arguments["reference"])
 
 	#
 	#Check validity of Kraken DB

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