[Biopython-dev] Bio.Motif update

[Michiel de Hoon]

Dear all,

As we discussed previously, I've been going over Bio.Motif to update it and make its usage more explicit. I'm pretty much done. While I have been uploading my changes to the main biopython github repository, this does not mean that these changes are final; comments and suggestions for changes are welcome.

In many cases, there is a difference in the syntax between the old Bio.Motif and the new Bio.Motif. For example, motif.consensus is a method in the old Bio.Motif, but a property in the new Bio.Motif.
While I tried to put PendingDeprecationWarnings on all changes consistently, there may be some corner cases that I missed.

For this reason, and also to make the documentation more understandable, it may be better to put the new Bio.Motif code in a module Bio.motifs, to put the old Bio.Motif code back into Bio.Motif (so that Bio.Motif in release 1.61 will be identical to the Bio.Motif in release 1.60), and (assuming that we are happy with the new Bio.motifs modules) put a PendingDeprecationWarning on Bio.Motif as a whole. Then in the documentation we'll have one chapter on Bio.Motif and one chapter on Bio.motifs. Also we'll have one set of tests for Bio.Motif, and one set of tests for Bio.motifs.

Any objections to creating a separate Bio.motifs module?

Here you can find the relevant chapter in the current documentation on the new Bio.Motif:

http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html#htoc190

Best,
-Michiel