Allow reference sequence to be returned always as upper case.

[mattions]

This is just a merge request to allow to return the sequence always as upper case, both in the raw and in the sequence format.

We have this user case in our case.

[landscape-bot]

Repository health increased by 0.15% when pulling 9e24c20 on mattions:allow_always_uppercase_seq into cd0fdea on mdshw5:master.

• No new problems were introduced.
• 1 problem was fixed (including 0 errors and 0 code smells).

[mdshw5]

Thanks for the pull request. If you add a test case for this (maybe here) then I'll merge and push a new PyPI release. It would also be great if you document this feature in the Readme.

[mattions]

As data tests,
is ok if I add a small bit of the hs37d5 in the data repo, or should I download the whole thing from somewhere and add it to the download_gene_fasta.py ?

I'm downloading the gens right now, if there is already an example with smaller case I could use that directly.

[mdshw5]

The script that generates the test data now generates a file called "genes.fasta.lower". This file should work for testing your contribution. You don't even have to test against a particular sequence, you could:

assert Fasta(sequence_always_upper=True)['gi|557361099|gb|KF435150.1|'] == Fasta()['gi|557361099|gb|KF435150.1|'].seq.upper()

and do the same for the as_raw case.

[mattions]

@mdshw5 I have updated the test to use genes.fasta.lower (and also make sure it gets created if you do not have it on the disk already.)

README updated with the example.

Should go green.

[mdshw5]

Looks great - thanks for the contribution!

[mattions]

do you have an idea when the next release with this fix will be out?

[mdshw5]

Thanks for reminding me. I just pushed the release through CI. When the tests pass a new version will be pushed to PyPI. Should happen some time this morning.

On Aug 3, 2015, at 7:18 AM, Michele Mattioni [email protected] wrote:

do you have an idea when the next release with this fix will be out?

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[mdshw5]

Looks like it's done.