^^how fast would this be for millions of sequences? also, here's my PDL code:


#!/opt/local/bin/perl

use Bio::Seq;
use Bio::DB::Sam;
use PDL;
use PDL::Char;
$PDL::SHARE = $PDL::SHARE;

# Load bam file
my $bamfile = Bio::DB::Sam->new( -bam => "eg1.bam" );
my @allReads = $bamfile->features( -type => 'match' );

for my $read (@allReads) {
    # Get read and target sequences
    ( $ref, $matches, $query ) = $read->padded_alignment;
    my $target = PDL::Char->new("$ref");
    for my $str ("$query") {
        my $match = PDL::Char->new($str);
        my @diff  = which( $match != $target )->list;
        # Print read name and mismatching positions
        print $read->qname,': ', "@diff\n";
    }
}

[download]

In reply to Re^2: mismatching characters in dna sequence by prbndr
in thread mismatching characters in dna sequence by prbndr

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.