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Fix bug when reading sequence names without whitespace, adding tests #19

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merged 3 commits into from
Aug 15, 2020

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cmorganl
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Thanks for writing such great software, Lianming! I really appreciate it.

I've attempted to fix that bug I reported and wrote a test to catch it. Some edits to the documentation are also included.

While mucking around with pyfastx I also noticed that the key_func feature may not be working as expected, but I may be mis-interpreting how it works exactly. Anyway, I wrote a test for key_func that checks whether the new identifiers (presumably stored as the 'name' attribute?) match a specific prefix ('contig') when parsing the FASTA file test.fa. This test is currently failing because it appears to me that no Sequence attributes are modified according to key_func.

Lastly, I included a few functions in tests/testing_utils.py to make retrieving test data more straightforward.

Thanks again!

@lmdu lmdu merged commit afd64b6 into lmdu:master Aug 15, 2020
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lmdu commented Aug 25, 2020

Thank you so much! I have fixed these bugs and released a new version

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2 participants