This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository qcumber.
commit 3bfb2d96e8a03e48491ff75050caed5914477ab4 Author: Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qcumber.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
