cigar string

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

hi all, i'm relatively new to perl and i'm just starting off with my first script to create a text based alignment viewer using the Bio_Samtools perl module. What i'm trying to do is parse a sam file to get all the reads that overlap a certain genomic window from the reference fasta sequence file. i have the following code to get all the reads that overlap a certain genomic window:

my @all_reads = $segment->features(
    -type   => 'match',
    -seq_id => $seq_ids[0],
    -start  => $window_start,
    -end    => $window_end,
    -filter => sub { shift->strand == -1 },
);
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i'm trying to recreate the real read sequence from its cigar string by adding insertions to the read (with a ^ character) and deletions (with a - character). i'm not exactly sure how to do this, since i can't access the cigar string. it seems to be stored in a reference to an array. see the following code:

for my $read (@all_reads) {
    print $read->qname,',',$read->aux_get("MD"), ',',$read->cigar_arra
+y,',', $read->strand, "\n";
};
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i don't know how to display the reference to the array denoted by the $read->cigar_array part of the code. it prints out ARRAY(0x100a2d058) or something similar instead of the split cigar string. once i get this working, i would need to add my desired characters to the read sequence to get to create the raw read. does anyone have any help? thanks!

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Re: cigar string by aaron_baugher (Curate) on Nov 29, 2011 at 05:06 UTC
According to the pod for the module, `$read->cigar_array` returns a reference to an array of arrays. You could print it with Data::Dumper to see its structure. You can dereference it to get at the top array like this: `@{$read->cigar_array}` . Then you can loop through that array of references, and dereference those to access those subarrays: `for my $toparray (@{$read->cigar_array}){ my( $operation, $count ) = @{$toparray}; # do stuff with this CIGAR operation and count }` [download] Aaron B. My Woefully Neglected Blog, where I occasionally mention Perl.	[reply] [d/l] [select]

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Re: cigar string
by aaron_baugher (Curate) on Nov 29, 2011 at 05:06 UTC

According to the pod for the module, $read->cigar_array returns a reference to an array of arrays. You could print it with Data::Dumper to see its structure. You can dereference it to get at the top array like this: @{$read->cigar_array} . Then you can loop through that array of references, and dereference those to access those subarrays:

for my $toparray (@{$read->cigar_array}){
  my( $operation, $count ) = @{$toparray};
  # do stuff with this CIGAR operation and count
}
[download]

Aaron B.
My Woefully Neglected Blog, where I occasionally mention Perl.

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