Writing alignments to file

[gusevfe]

Is it possible to write alignments to file?

E.g. I want to process an existing .bam file by removing a part of the sequence. How do I do that?

[danmaclean]

Hi, can you clarify what you require. I guess you want to process an alignment, removing some of the sequence, create a new Bio::DB::Alignment object and write that to a new BAM file? Or are you trying to do something more complicated?

cheers

[gusevfe]

That's exactly what I want.

On Thu, Feb 16, 2012 at 2:13 PM, danmaclean <
[email protected]

wrote:

Hi, can you clarify what you require. I guess you want to process an
alignment, removing some of the sequence, create a new Bio::DB::Alignment
object and write that to a new BAM file? Or are you trying to do something
more complicated?

cheers

---

Reply to this email directly or view it on GitHub:
#10 (comment)

Kind regards,
Fedor Gusev.

[danmaclean]

The official samtools C API function for writing to BAM isn't implemented yet, as it is a bit complicated and we considered most users would want to use BAM as a datasource much more than as a sink. The workaround is to use the Bio::DB::Alignment#to_s method that writes the alignment object in SAM, which you can convert to BAM the old fashioned way. We are working on making BAM writable.

cheers