[Biopython-dev] Proteomics/Mass Spec in Biopython

[Chris Mitchell]

Hi everyone,

I recall some time ago there was an email about getting some mass spec
functionality within BioPython.  I started a BioPython branch to
incorporate some iterators for common file types.  Of note, there is an
iterator for .msf files created by Proteome Discoverer, which thankfully is
light-years faster than using PD (and much more forgiving on memory...).

It's located here:
https://github.com/chrismit/biopython/tree/Proteomics

It's following along the progression of my spectra viewer, which is hosted
on the same repository (which, for anyone using linux might want to look
at; I couldn't find a spectra viewer I liked for linux.).  As I generalize
more of the methods within that program I'll be adding them to the
BioPython branch.  Also, I'll be putting in some methods to take care of
other common tasks such as FDRs calculation from the input files.

I'd love to hear if anyone else wants to join up on this branch or provide
suggestions.

Chris