[Bioperl-l] Fasta counting script?

Dave Messina David.Messina at sbc.su.se
Tue Nov 22 03:08:11 EST 2011

Hi Kylie,

You can use the length method for this.

my $seq_length = $seq_obj->length();

Have you taken a look at the beginner's HOWTO? There's a nice table of
sequence methods as well lots of other good information in there.



On Tue, Nov 22, 2011 at 03:23, Kylie Goodyear <goodyearkl at gmail.com> wrote:

> Hi,
> 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
> formats
> 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) {
>    $count++;
> }
> #Display the number of sequences present
> print "There are $count sequences present.\n";
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