[Bioperl-l] Length of a sequence.

Staffa, Nick (NIH/NIEHS) [C] staffa at niehs.nih.gov
Fri Sep 8 10:13:31 EDT 2006


Wondering why I'm having trouble finding out how to get the total length of a sequence.
I am doing wonderfully parsing all the features information.
y'd think this would be simple.
What's the best thing to do?


use Bio::SeqIO;
#       Get the sequence 
...
$seqio_object = Bio::SeqIO->new(-file => "$filename" );  
$seq_object = $seqio_object->next_seq; 
>>> What's the magic code to put HERE????<<<<<<<<<<<<<<<<<<<
print "Sequence $fileroot has length $len\n";
#       Get the features as an array of objects 
#       This seems to get them all. Makes an array of objects.
my @features = $seq_object->get_SeqFeatures(); # just top level



Nick Staffa
Telephone: 919-316-4569  (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina




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