phac-nml / biohansel

Rapidly subtype microbial genomes using single-nucleotide variant (SNV) subtyping schemes
Apache License 2.0
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Cannot parse gzipped seq files on Mac OSX since zcat doesn't work the same as under Linux #39

Closed peterk87 closed 6 years ago

peterk87 commented 6 years ago

Probably related to the issue described here:

https://serverfault.com/questions/570024/zcat-gzcat-works-in-linux-not-on-osx-general-linux-osx-compatibility

Changing the following line https://github.com/phac-nml/bio_hansel/blob/master/bio_hansel/parsers.py#L94

from

with os.popen('zcat {}'.format(filepath)) as f:

to

with os.popen('zcat < {}'.format(filepath)) as f:

May solve this issue, but testing on OSX is required.