[Biopython-dev] [Bug 2905] Short read alignment format SAM / BAM

[Peter]

On Thu, Jul 15, 2010 at 6:20 PM, Vince S. Buffalo wrote:
> Sorry to bump this old topic, but are there plans to merge this into the
> main project? I do a lot of processing with the SAM format and it would be
> great to use Biopython for this.
>
> Does the pure Python implementation run as quickly as the pysam
> version? Is anyone still considering forking pysam and rewriting the
> C wrappers?
>
> Vince

EMBOSS now has limited SAM/BAM support,
http://lists.open-bio.org/pipermail/emboss-dev/2010-July/000656.html

BioLib is also now taking an interest in SAM/BAM support,
I'd expect to see something on their mailing list soon:
http://biolib.open-bio.org/wiki/Main_Page

Can I ask what you want to do with SAM/BAM files?

I did quite a bit of exploratory work for SAM/BAM in SeqIO,
focussing on the raw reads (not the alignment side). This
is very different from what you can do with PySam. It has
allowed me to do SAM/BAM back to FASTQ which has been
helpful in real work. There are branches on github, but still
quite experimental and not necessarily going to be committed:
http://github.com/peterjc/biopython/tree/seqio-sam-bam
http://github.com/peterjc/biopython/tree/seqio-sam-bam-index

Peter