[Biopython-dev] Parsing TRANSFAC matrices with Bio.Motif

[Michiel de Hoon]

Dear all,

Currently Bio.Motif has some support for writing TRANSFAC files but not for reading TRANSFAC files. I would like to add such a parser to Bio.Motif. Do you all agree that it fits in this module? Note that the TRANSFAC files very much look like EMBL files, and therefore contain much more information than what is currently in a Bio.Motif._Motif.Motif object (the object to be generated by Bio.Motif.read(handle, "transfac")). Perhaps the easiest is to add an attribute .annotations to Bio.Motif._Motif.Motif objects, and use it as a dictionary to store the EMBL-like annotations under their 2-letter keys.

On a related note, currently Bio.Motif._Motif.Motif objects also perform functions that are more appropriate for a separate PWM (position-weight matrix) class within Bio.Motif. It may be a good idea to have a separate PWM class for this functionality.

Best,
-Michiel.