[Bioperl-l] Fasta counting script?

[Smithies, Russell]

Or again, you could use the builtin scripts bp_seq_length.pl or bp_gccalc.pl
As previous posters have hinted, RTFM - the answers are all in there!

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Fields, Christopher J
> Sent: Wednesday, 23 November 2011 5:13 a.m.
> To: Kylie Goodyear
> Cc: <bioperl-l at bioperl.org>
> Subject: Re: [Bioperl-l] Fasta counting script?
> 
> This sounds a little homework-y.  Sure this isn't for a class? :)
> 
> One clue (and a good thing to keep in mind): always 'use strict; use warnings;'
> with your scripts if you are new to perl.  Doing so would let you know there is
> a problem with the script the way it is written, specifically, the place where
> you are inquiring about the length.
> 
> chris
> 
> On Nov 22, 2011, at 7:00 AM, Kylie Goodyear wrote:
> 
> > 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";
> >>
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> >>
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> 
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