[Biopython-dev] MAF Parser/Writer/Indexer

[Sczesnak, Andrew]

Hi Brad,

> We may want to take a look at the interval access functionality in
> bx-python and MAF parsing tied in with this:
>
> https://bitbucket.org/james_taylor/bx-python/src/tip/lib/bx/interval_index_file.py
> https://bitbucket.org/james_taylor/bx-python/src/tip/lib/bx/align/maf.py

The interval indexing scheme in bx-python seems really nice.  By dropping
intervals into bins, a la UCSC MySQL tables, and using a compact file format
instead of SQLite, I'm sure it's quite fast.

> It would be useful to have an API that queries across bx-python intervals,
> BAM intervals and other formats.

I agree, I think it would be great if we could implement some sort of API for
indexing and accessing intervals in SAM/BAM, MAF, ACE, and really, any
format that can be made to report an offset and set of interval coordinates.
Even a multifasta can have interval information in the header that a user
could extract and pass to the indexer with a callback function.  Gene annotation
files, like GFF, have this information too.

What would make the most sense here?  Would a more general interval indexing
and searching module be too much?  I feel like a task I'm always performing is
searching various files by chromosome, start, and stop.

Example: A BED file of ChIP-Seq peaks called by MACS--are there any peaks
overlapping gene X?

Example: How many alignments are there in an RNA-Seq BAM file that overlap
rRNA and tRNA annotations in a GFF file, presumably from contaminating RNA?


Andrew

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