[Bioperl-l] Length of a sequence.

skirov skirov at utk.edu
Fri Sep 8 10:41:34 EDT 2006


Sorry, I meant perldoc Bio::Seq of course (/search length) or you can do plain 
length($seq_object->seq);
My point is - read the object documentation first- it would have most answers 
to your questions.

>===== Original Message From "Staffa, Nick (NIH/NIEHS) [C]" 
<staffa at niehs.nih.gov> =====
>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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