rkk has asked for the wisdom of the Perl Monks concerning the following question:

Hello, I am using BIO::DB::SAM perl module to parse binary file. Here is my code. 

#!/usr/bin/perl
use strict;
use Bio::DB::Sam;
open (OUTPUT1,">op_info.txt") || die "can't: $!";
my $bam = Bio::DB::Bam->open('input.bam');
my $header       = $bam->header;
my $target_count = $header->n_targets;
my $target_names = $header->target_name;
while (my $align = $bam->read1)
{
print OUTPUT1 "$align\n";
}

output:



Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194d8)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194c0)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194d8)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194c0)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194d8)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194c0)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194d8)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194c0)
Bio::DB::Bam::Alignment=SCALAR(0x7fe4d0b194d8)

[download]

How to dereference the variable and print the contents of the file.

Thanks in advance.

Replies are listed 'Best First'.
Re: De referencing
by poj (Abbot) on Jun 22, 2013 at 07:01 UTC
    From the docs; 
    $alignment = $bam->read1()
Read one alignment from the BAM file and return it as a Bio::DB::Bam::
+Alignment object.

    [download]

    You need to use the methods in Bio::DB::Bam::Alignment to access the information. For example 

     while (my $align = $bam->read1) {
    my $seqid  = $align->seq_id;
    my $start  = $align->start;
    my $end    = $align->end;
    my $strand = $align->strand;
    my $ref_dna= $align->dna;
}

    [download]

    poj
[reply]
[d/l]
[select]
Re: De referencing
by davido (Cardinal) on Jun 22, 2013 at 06:00 UTC

    Assuming the scalar ref held in $align is simple, and not just the head of some more complex structure (or object)...

    print OUTPUT1 "$$align\n";

    [download]

    If it's the head of something more complex, use Data::Dumper to get a look at the structure, or read the module POD so you can plan how to dereference it effectively.

    A nice introduction to references is found in perlreftut.


    Dave

[reply]
[d/l]
[select]
Re: De referencing
by aitap (Curate) on Jun 22, 2013 at 07:00 UTC
    Your $align variable is actually a Bio::DB::Bam::Alignment object, so instead of stringifying it you have to call its methods and do something with their return values. You'll probably want to print $align->query->dna.
[reply]
[d/l]
[select]
Re: De referencing
by locked_user sundialsvc4 (Abbot) on Jun 22, 2013 at 22:25 UTC

    One good tool for sorting this sort of thing out, in a general sense, is Data::Dumper, which is good at printing-out any ol’ thing so that you can see what it is.   Once you can see it, you can probably see your way clear (along with taking a good re-look at the documentation) as to how to properly de-reference it and use it.

    use Data::Dumper;
    print STDERR Data::Dumper->Dump([ $align ], [ 'align' ]);

    The STDERR (“standard error-output”) stream is a traditional place to send error-messages and “chatty” in-progress status messages.   It normally maps to the terminal, or, in the case of Apache, to the error-log.

    In this case, though, the documentation example for Bio::DB::Sam ought to be sufficient.   In their example, read1 clearly returns an object ... and the documentation obliquely says (without actually saying), that this object is a Bio::DB::Bam::Alignment object, which is separately documented in CPAN.   When the documentation does not go that far, Data::Dumper will usually give you the important-clue by having identified the object class-name that a particular variable has been bless()ed into.   A search for that class-name on CPAN, more often than not, will be fruitful.

      How do you complete align record. For instance I would like to print all the align record as it is in sam file if it satisfies a particular condition.
[reply]
        YEs I kind of have same qn....how to print complete record
[reply]

Back to Seekers of Perl Wisdom