[Bioperl-l] from SimpleAlign to SAM/BAM

[Dan Bolser]

On 19 May 2010 17:40, Lincoln Stein <lincoln.stein at gmail.com> wrote:
> Bio::Samtools, which is separate from bioperl but compatible with it,
> provides read/write access to SAM and BAM via Heng's C library.

If I understand correctly, Bio::Samtools is a meta package that
encompasses Bio::DB::Sam and friends. However, when I look at
Bio::DB::Sam, I only see "Read SAM/BAM database files", not write, and
I don't see how to write SAM files from the docs there.

I just looked at the pod for Bio::Assembly::IO::sam (how come this
isn't documented in CPAN?), and I read:

This is a (currently) read-only IO module designed to convert
Sequence/Alignment Map (SAM) ...

I guess this is what was being discussed on in this thread (the fact
that IO doesn't yet write, but XS can be used to get it writing).

Did I understand correctly, or is there some way to write SAM from BioPerl?


Cheers,
Dan..

> Lincoln
>
> On Wed, May 19, 2010 at 9:34 AM, Mark A. Jensen <maj at fortinbras.us> wrote:
>
>> Albert-- have a look at Bio::Tools::Run::Samtools which incorporates the
>> use of Bio::Assembly::IO::sam (I think). I know there is only read
>> capability for B:A:I:sam, but Samtools may give you the appropriate wrapper
>> for doing writes (some assembly (so to speak) required...)-- cheers MAJ
>> ----- Original Message ----- From: "Albert Vilella" <avilella at gmail.com>
>>
>> To: <bioperl-l at bioperl.org>
>> Sent: Wednesday, May 19, 2010 4:36 AM
>>
>> Subject: [Bioperl-l] from SimpleAlign to SAM/BAM
>>
>>
>>  Hi,
>>>
>>> I would like to know what would be the best way to generate a SAM/BAM file
>>> with cDNA alignments against the human reference from a bunch of
>>> Bio::SimpleAlign
>>> cDNA multiple sequence alignment objects.
>>>
>>> Considering I've got a way to map the cDNAs to chromosome coordinates,
>>> how can I generate a SAM/BAM file with ~1,000,000 entries against ~23.000
>>> human
>>> coordinates?
>>>
>>> As far as I can see, there is an Bio::Assembly::IO::sam.pm which loads
>>> assemblies.
>>> Should I be using some other tool existing not in bioperl?
>>>
>>> Cheers,
>>>
>>> Albert.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
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>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
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