fix for GFFs with ##FASTA section in python 3.7

daler / gffutils

GFF and GTF file manipulation and interconversion

http://daler.github.io/gffutils

MIT License

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fix for GFFs with ##FASTA section in python 3.7 #142

Closed pbradz closed 4 years ago

pbradz commented 5 years ago

Apparently in Python 3.7 the behavior of StopIteration changes such that gffutils=0.9 crashes with a "RuntimeError: generator raised StopIteration" exception in iterators.py whenever a GFF file is loaded that contains a ##FASTA section at the end with sequences. I wrapped the offending statement in a try/except as suggested here; that seems to fix the problem.

(This is my first pull request so sorry in advance if I'm doing something wrong!)

mr-c commented 5 years ago

@pbradz Does https://github.com/daler/gffutils/pull/121 fix that for you?

pbradz commented 5 years ago

Looks like it does, thanks!

On Tue, Sep 24, 2019 at 5:45 AM Michael R. Crusoe notifications@github.com wrote:

@pbradz https://github.com/pbradz Does #121 https://github.com/daler/gffutils/pull/121 fix that for you?

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daler commented 4 years ago

Closing in favor of #121