Here's a solution using Bioperl: 
#!/usr/bin/perl -w

use strict;
use Bio::SeqIO;

my @files   = <*.seq>;
my $pattern = '([AN]*)';

foreach my $file (@files) {
   my $seqio = Bio::SeqIO->new( -file => $file );
   while ( my $seqobj = $seqio->next_seq() ) {
       my $raw_seq = $seqobj->seq();
       my @length_of_matches;

       while ( $raw_seq =~ /$pattern/og ) {
           push @length_of_matches, length $1;
       }

       @length_of_matches = sort { $b <=> $a } @length_of_matches;
       print $length_of_matches[ 0 ], ' ', $file, "\n";
   }
}

[download]
Using Bioperl for easy scripts likes this is a good idea, because it allows you to very easily port your program to almost any sequence file format known to man.

In reply to Re: Count Occurrences of a string by biosysadmin
in thread Count Occurrences of a string by MiamiGenome

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