new method rename-chr for gff2gff.py

[kevinrue]

Equivalent to previous PR for gff2gff.

Please do not merge until unit tests are implemented.

@sebastian-luna-valero : I assume this is about adding more entries in https://github.com/CGATOxford/cgat/blob/master/tests/gff2gff.py/tests.yaml ?

[kevinrue]

Let's see if I guessed correctly, about those unit tests. Haven't played with this kind of YAML setup before.

[sebastian-luna-valero]

Thanks!

Let's wait and see what travis says.

Did you also add the chip_peaks.bed file to the folder?

[sebastian-luna-valero]

Sorry, just realised that the chip_peaks.bed is already there.

I think you need to use %DIR% for your ucsc2ensemble.txt input file to get the tests passing; i.e.:

options: --method=rename-chr --rename-chr-file=%DIR%/ucsc2ensembl.txt

rather than:

options: --method=rename-chr --rename-chr-file=ucsc2ensembl.txt

[kevinrue]

Oops. Didn't spot that one in the other examples. Funny how input/reference files don't need that. I can see why that would be, despite the confusion.

[kevinrue]

Tada!!
Thanks for the help @sebastian-luna-valero !

[sebastian-luna-valero]

Great!

Before merging, could you please update this branch with the latest master? I have added in a couple of more tests, and I would like to see if this branch is ok with that.

Best regards,
Sebastian

[sebastian-luna-valero]

Thanks, @kevinrue

You got pep8 errors. To reproduce the problem locally, just run: nosetests -v tests/test_style.py

You can then do: pep8 CGAT/scripts/gff2gff.py to find out where the error is.

Here is a table with the error codes explained:
https://pep8.readthedocs.io/en/1.4.6/intro.html#error-codes

Please let me know if you need further help.

Best regards,
Sebastian

[kevinrue]

Yep, I just saw that this morning. I know PEP8, but I didn't remember that there was a command for that. I'll make sure to use it on develop directly in PyCharm, in the future. Stand by while I correct this :)

…

On Fri, Apr 6, 2018 at 8:59 AM, Sebastian Luna-Valero < ***@***.***> wrote: Thanks, @kevinrue <https://github.com/kevinrue> You got pep8 errors. To reproduce the problem locally, just run: nosetests -v tests/test_style.py You can then do: pep8 CGAT/scripts/gff2gff.py to find out where the error is. Here is a table with the error codes explained: https://pep8.readthedocs.io/en/1.4.6/intro.html#error-codes Please let me know if you need further help. Best regards, Sebastian — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#390 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFgHlFU4HaFJXoLV1bGaClPfwod0QqxIks5tlyBHgaJpZM4TIl3-> .

[sebastian-luna-valero]

No worries, no rush.

Just wanted to make sure that the failed tests were not stopping you ;)

[kevinrue]

Did you disable some of the PEP8 checks for the CI?
I spotted and fixed the rules that my new lines broke, but pep8 also pointed out some existing lines that are >80 characters wide, e.g.:

• https://github.com/kevinrue/cgat/blob/master/CGAT/scripts/gff2gff.py#L164
• https://github.com/kevinrue/cgat/blob/master/CGAT/scripts/gff2gff.py#L828
  I don't really know how to solve those as they are somewhat naturally long lines.

[sebastian-luna-valero]

Yes, some PEP checks are skipped:
https://github.com/CGATOxford/cgat/blob/master/tests/test_style.py#L32

That's why running nosetests -v tests/test_style.py should give you the same answer as the CI.

Best regards,
Sebastian

[kevinrue]

Seems to be ready to go 🎉

[sebastian-luna-valero]

Thanks again!