Re: Count Occurrences of a string

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.

Comment on Re: Count Occurrences of a string Download Code

Replies are listed 'Best First'.
Samples Help, Thank you by MiamiGenome (Sexton) on Sep 10, 2003 at 14:38 UTC
Dear Perl Monks, Thank you all for your constructive and instructive help. I am dealing with 2 conflicting, yet synergistic issues in my research, namely 1. getting my analyses completed, and 2. learning BioPerl/Perl. For nearly all my scripting, I am whip out quick jiffies to answer the questions of our genome center, but as my BioPerl comes up to speed, I sporadically need more guidance. I again thank you all. (No, my question wasn't homework :) )	[reply]
Re: Samples Help, Thank you by biosysadmin (Deacon) on Sep 10, 2003 at 14:58 UTC
Good luck with your research.In addition to Perl Monks, a good resource for learning BioPerl is the doc.bioperl.org website, and the BioPerl mailing lists. Your name suggests that we may have a mutual friend in common, do you know Ken Rudd at the University of Miami? If so, tell him that Tex Thompson from the Rochester Institute of Technology says hello. :)	[reply]