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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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accommodate slashes in species names #18

Closed katholt closed 9 years ago

katholt commented 9 years ago

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

katholt commented 9 years ago

Fixed. Available now in master, will be in release 0.1.5.