[Bioperl-l] Are Bio::DB::Bam::Alignment objects read-only ?

[Lincoln Stein]

Unfortunately l_qseq read/writes the length of the query sequence, not the
sequence itself.

Lincoln

On Thu, Nov 24, 2011 at 3:26 AM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> According to the docs the low-level API for Bio-Samtools, both read and
> write are allowed:
>
> http://search.cpan.org/perldoc?Bio::DB::Sam#The_low-level_API
>
> Using the low-level API for this purpose isn't documented as well, though
> (the high-level API is read only AFAICT).
>
> The error message is a standard one generated from the XS bindings where
> the passed argument passed isn't mapped correctly.  Looking through the
> Sam.xs file, qseq() is only prototyped as a reader; the only arg is a
> Bio::DB::Bam::Alignment (e.g. $self).  However, it appears there is a
> function specified for Bio::DB::Bam::Alignment names l_qseq() that might be
> the setter, wheras qseq() is maybe to be the getter (ignore the 'bama_'
> prefix):
>
> ....
>
> int
> bama_l_qseq(b,...)
>    Bio::DB::Bam::Alignment b
> PROTOTYPE: $;$
> CODE:
>    if (items > 1)
>      b->core.l_qseq = SvIV(ST(1));
>    RETVAL=b->core.l_qseq;
> OUTPUT:
>    RETVAL
>
> SV*
> bama_qseq(b)
> Bio::DB::Bam::Alignment b
> PROTOTYPE: $
> PREINIT:
>    char* seq;
>    int   i;
> CODE:
>    seq = Newxz(seq,b->core.l_qseq+1,char);
>    for (i=0;i<b->core.l_qseq;i++) {
>      seq[i]=bam_nt16_rev_table[bam1_seqi(bam1_seq(b),i)];
>    }
>    RETVAL = newSVpv(seq,b->core.l_qseq);
>    Safefree(seq);
> OUTPUT:
>    RETVAL
>
>
> -chris
>
> On Nov 23, 2011, at 10:02 AM, Cook, Malcolm wrote:
>
> > Charles,
> >
> > I suggest you reconsider your approach to rather, use `samtools view` to
> pipe your reads to stdout in sam format, then stream edit the barcode and
> pipe it back to samtools for conversion back to .bam file.
> >
> > I know this is not what you're asking.  I'm pretty sure that direct
> answer to your question is, "yes - they are read-only".
> >
> > ~Malcolm
> >
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> >> bounces at lists.open-bio.org] On Behalf Of Charles Plessy
> >> Sent: Wednesday, November 23, 2011 4:28 AM
> >> To: bioperl-l at bioperl.org
> >> Subject: [Bioperl-l] Are Bio::DB::Bam::Alignment objects read-only ?
> >>
> >> Dear BioPerl developers,
> >>
> >> I am trying to process some unaligned paired-end reads with
> Bio::DB::Sam.
> >> For
> >> each pair, I want to detect a sequence index and a unique molecular
> >> identifier in
> >> the linker, record them as auxiliary flags, and trim the linker from
> the read.
> >>
> >> I collect the pairs through a features iterator, and can access all
> their data
> >> through the high-level Bio::DB::Bam::Alignment API.  After modifying
> them
> >> (linker trimming and adding flags), I want to write the resulting pairs
> as a
> >> new unaligned BAM file.
> >>
> >> I apologise if the solution is trivial, but my problem is that I do not
> manage to
> >> modify the Bio::DB::Bam::Alignment objects.  Typically, attempts such as
> >> “$pair[0]->qseq("GATACA")” give errors like
> >> “Usage: Bio::DB::Bam::Alignment::qseq(b) at
> >> /usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm line 80”.
> >>
> >> Since I did not find explanations or portsions of source code
> indicating how to
> >> modify Bio::DB::Bam::Alignment objects, I wonder if they are read-only…
> >>
> >> Have a nice day,
> >>
> >> --
> >> Charles Plessy
> >> Tsurumi, Kanagawa, Japan
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > _______________________________________________
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>
>
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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>