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

Cook, Malcolm MEC at stowers.org
Wed Nov 23 11:02:26 EST 2011


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".


> -----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
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> Bioperl-l at lists.open-bio.org
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