[Bioperl-l] Fasta counting script?

[Kylie Goodyear]

Thank you for your help. It keeps telling me that it can't find
"length" do you think it has to do with the way I am coding it?

#!/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 $countseq=0;
while (my $seq_obj = $seqio_obj->next_seq, ) {
    $countseq++;
    }
#Display the number of sequences present
print "There are $countseq sequences present.\n";

#Count number of charcaters in file
my $seq_length = $seq_obj->length ;
print $seq_length


On Nov 22, 5:08 am, Dave Messina <David.Mess... at sbc.su.se> wrote:
> 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.
>
> http://www.bioperl.org/wiki/HOWTO:Beginners
>
> Dave
>
>
>
>
>
>
>
>
>
> On Tue, Nov 22, 2011 at 03:23, Kylie Goodyear <goodyea... 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";
>
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioper... at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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