[Bioperl-l] Fasta counting script?

Kylie Goodyear goodyearkl at gmail.com
Mon Nov 21 21:23:13 EST 2011

This may seem like a stupid question but I am just learning bioperl
and I am trying to figure out how to get a count of all the characters
in my FASTA file. I manged to get the number of sequences using the
following. Is there a way to tell bioperl to count the characters?

#!/usr/bin/perl -w
#Defines perl modules
#Bio::Seq deal with sequences and their features
use Bio::Seq;
#Bio::SeqIO handles reading and parsing of sequences of many different
use Bio::SeqIO;
#Read FASTA file
$seqio_obj = Bio::SeqIO->new(-file => "DNA_sequences.fasta", -format
=> "fasta" );
#Count how many sequences are present in file
my $count=0;
while (my $seq_obj = $seqio_obj->next_seq) {
#Display the number of sequences present
print "There are $count sequences present.\n";

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