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mdshw5 / pyfaidx

Efficient pythonic random access to fasta subsequences
https://pypi.python.org/pypi/pyfaidx
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Update __init__.py #216

Closed rraadd88 closed 8 months ago

rraadd88 commented 8 months ago

Hi, I added a command to convert gzip to bgzip in the error message of UnsupportedCompressionFormat. It should be helpful for those who encounter this error.

mdshw5 commented 8 months ago

Thanks for the thoughtful contribution. I do think this will help a few people, since "how to bgzip a file" is still a common bioinformatics question!

jmarshall commented 8 months ago

However samtools bgzip is not a samtools subcommand so this will not in fact work.

I would recommend instead

For example: gunzip file.fa.gz; bgzip file.fa

This is simpler, avoids shell redirection, and avoids confusion about the file name extension used.

mdshw5 commented 8 months ago

@jmarshall are you like Beetlejuice but for samtools? 😂

Of course this is a great recommendation and I’ll make the change.

jmarshall commented 8 months ago

🤣 First time I've ever got any value out of the GitHub dashboard feed — it showed you had made a new release surprisingly soon after the last one, so I had a look…

mdshw5 commented 8 months ago

I truly appreciate it. I thought I had just fallen behind in the latest block gzip compression methodology!