[Bioperl-l] Can't get length

James Thompson tex at biocompute.net
Wed Jan 5 20:56:53 EST 2005


Try using $seq->length() instead of $seq.length(). If you still have problems,
mail the list again and be sure to include your input file. Also, unless you're
using a very large sequence file, use the 'fasta' format rather than the
'largefasta' format.

Cheers,

James Thompson

On Thu, 6 Jan 2005, kishua2000 kishua wrote:

> Hello,
>  
> I'm using seqIO object to load a DNA sequence in a fasta-like format (">"
> + some info, in the header). The header doesn't contain any info about
> the length of the sequence.
>  
> $in  = Bio::SeqIO->new(-file =>$fastaFile , '-format' => 'largefasta');
> Then I load my sequence to a seq object
>  
> my $seq = $in->next_seq()
>  
> but when I try to get the length of the sequence I get 0
>  
> $len=$seq.length(); #----> 0
>  
> so how to get simple length ?
>  
> 
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