[Bioperl-l] Fasta counting script?

[Fields, Christopher J]

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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>>> Bioper... at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
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