in reply to input record separator help

I've been making small modification of your code: 

while (<INFILE>)   {
    if (/^>/) { 
        $in_sequence = 1;
        next; 
    }      
 
    $dna .= $_ if $in_sequence;              }
}

[download]

Also, I'd like to suggest you look at site of BioPerl if you haven't seen yet it ;)

~ Schiller

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Re: Re: input record separator help
by Anonymous Monk on Mar 15, 2004 at 14:29 UTC
    thanks for your help Schiller, but I dont get how I can perform my various calculations on each sequence using your code. How can I push each extracted $dna into an array, which I can then iterate through for the calculations? This is the sort of thing I want to do for each sequence: 
    for (my $i=0; $i < @genome; $i++)  {

     my $token = $genome[$i] . $genome[$i+1];
     $freq{$token}++;
     $tt = $freq{tt};
     $cg = $freq{cg};
     $gc = $freq{gc};
     $ta = $freq{ta};
     $at = $freq{at};
     $cc = $freq{cc};
     $tg = $freq{tg};
     $ag = $freq{ag};
     $ac = $freq{ac};
     $ga = $freq{ga};
     $aa = $freq{aa};
     $gg = $freq{gg};
     $ca = $freq{ca};
     $ct = $freq{ct};
     $gt = $freq{gt};
     $tc = $freq{tc};

}

    [download]
    I have tried just using a simple 'push', but this slowed the program down far too much. cheers x
[reply]
[d/l]
      Anonymous Monk,
      So my earlier assumption that you wanted to throw away non sequence lines was correct. I believe you can avoid an array all together. 
      #!/usr/bin/perl
use strict;
use warnings;

my $file = $ARGV[0] || 'default';
open (DNA, '<', $file) or die "Unable to open $file for reading : $!";
my %seq;

while ( <DNA> ) {
    my $dna = <DNA>;
    my $pairs = "a2" x ((length $dna) / 2);
    $seq{$_}++ for unpack $pairs , $dna;
}
print "$_ : $seq{$_}\n" for keys %seq;

      [download]
      Cheers - L~R
[reply]
[d/l]
        hi L~R, thankyou for your help, would you mind exaplaining to me exactly what the code does? e.g. the 'a2' and 'unpack' bits? many thanks
[reply]

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