From: Paul Cherng ppcherng@gmail.com
Date: 30 November 2014 08:46:47 GMT+11
To: drkatholt@gmail.com
Subject: SRST2 getmlst.py bug
Hi Dr. Holt,
I am using your SRST2 software and I have come across a bug with the getmlst.py script. It appears that the "Campylobacter concisus/curvus" species from http://pubmlst.org/data/ causes the script to crash because of the slash in the name. Here is the error I get:
Traceback (most recent call last):
File "/usr/local/bin/getmlst.py", line 183, in
main()
File "/usr/local/bin/getmlst.py", line 141, in main
species_all_fasta_file = open(species_all_fasta_filename, 'w')
IOError: [Errno 2] No such file or directory: u'Campylobacter_concisus/curvus.fasta'
I'm not sure what the best solution for this is, perhaps simply replacing slashes with underscores will suffice.
From: Paul Cherng ppcherng@gmail.com Date: 30 November 2014 08:46:47 GMT+11 To: drkatholt@gmail.com Subject: SRST2 getmlst.py bug
Hi Dr. Holt,
I am using your SRST2 software and I have come across a bug with the getmlst.py script. It appears that the "Campylobacter concisus/curvus" species from http://pubmlst.org/data/ causes the script to crash because of the slash in the name. Here is the error I get:
getmlst.py --species "Campylobacter concisus/curvus"
Traceback (most recent call last): File "/usr/local/bin/getmlst.py", line 183, in
main()
File "/usr/local/bin/getmlst.py", line 141, in main
species_all_fasta_file = open(species_all_fasta_filename, 'w')
IOError: [Errno 2] No such file or directory: u'Campylobacter_concisus/curvus.fasta'
I'm not sure what the best solution for this is, perhaps simply replacing slashes with underscores will suffice.
Thanks, -Paul Cherng