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 },
);
[download]

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";
};
[download]

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!

Comment on cigar string Select or Download Code

Replies are listed 'Best First'.

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]


P is for Practical
	PerlMonks