[Bioperl-l] Bio::Tools::SeqStats to count bases

[Fields, Christopher J]

Please make sure and read both Roy's and Adam's responses all the way through; Bio::SeqIO is not a sequence object but the front-end for format parsing (e.g. FASTA, etc).  Bio::PrimarySeq does not have a '-file' parameter, Bio::SeqIO does.  

If SeqStats truly doesn't work with Bio::Seq we can fix that, but according to Adam he has tested using Bio::SeqIO out and it seems to work.

chris

On Feb 4, 2013, at 12:02 PM, Slym <whereverroadgoes at gmail.com>
 wrote:

> The thing is, if I use Bio::SeqIO then  Bio::Tools::SeqStats produces an 
> error (saying that it wants input provided by Bio::PrimarySeq).
> (btw in this line
> $seqobj = Bio::PrimarySeq->new( -file => "sekw2.fasta", - alphabet => 
> 'dna',); 
> there's a typo "sekw2" instead of "seq2" but this is correct in my original 
> code).
> 
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