[Bioperl-l] First cut svn repository [was Re: SVN and ...Re: Perltidy]

Nathan S. Haigh n.haigh at sheffield.ac.uk
Sat Jun 30 13:25:58 EDT 2007


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

- -- snip --
> 
> 
>> There seems to be a plethora of file naming styles which means there's
>> a pretty long list of non-standard extensions. So at some point
>> someone will commit a new data file with a new extension (often
>> describing what program created the output or the test for which it's
>> intended) that won't be in the auto-props file - can you think of a
>> way around this?
> 
> Ive been thinking about this a bit. How about this?
> 
> - We have just "standard" files and extensions (like *.blast, *.fasta)
> in the auto-props list.

I think the list of seq formats recognised by Bioperl in Bio::SeqIO and
Bio::AlignIO would be a good start. As these are likely to be the ones
that are sensitive to file format recognition and thus could break tests
if renamed.

I think a lot of people have used "." in file names as an alternative to
a space. I think it would be beneficial to use an underscore "_" in
these cases and leave the "." to represent the beginning of the file
extension.

> 
> - We manually add props for the files that have nonstandard, arbitrary
> extensions so all the files that we currently have now are prop'd.
> 
> - At some point we rename those nonstandard files to have standard
> extensions. Especially for the t/data/ files, we'll have to make sure to
> update the tests that rely on them.

Nice and easy with svn :)
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.6 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGhpHiczuW2jkwy2gRAuZ5AKCnd2MvCsvSn1NemDVMmabnieR2vACg1Qk0
pYVvXwxq0lpiGfM09RQ6A1I=
=3Lhw
-----END PGP SIGNATURE-----


More information about the Bioperl-l mailing list