[Bioperl-l] RE: :SeqIO HOWTO

Barry Moore bmoore at genetics.utah.edu
Thu Nov 3 11:52:26 EST 2005


If I understand you question correctly, you are asking if the variable
that contains the sequence(s) ($inseq in your script) from you sequence
file is a string (called a scalar in perl) as opposed to an array.  The
answer is "neither".  The variable $inseq is a hash based Bio::SeqIO
object that holds the details for reading sequences from your sequence
file.  One of the methods associated with that object is next_seq which
returns then next sequence in you file. Actually it returns another hash
based object - a Bio::Seq object which contains all the details about
the next sequence in the file.  That Bio::Seq object has a number of
methods associated with it which allow you to retrieve details like
display id and sequence.  So while $inseq is neither a scalar nor an
array, in terms of what it can do, it would be better to think of it in
terms of an array because it can read a file with many sequences in it,
and you can step through those sequences with next_seq like you would
step through the elements in an array with a for each loop.  Hope I
answered the correct question.


P.S.  Try to remember to reply-all so that your questions go to the
list, and not only to me.  That way others can contribute to the
discussion as well.

> -----Original Message-----
> From: chen li [mailto:chen_li3 at yahoo.com]
> Sent: Thursday, November 03, 2005 2:05 AM
> To: Barry Moore
> Subject: Bio::SeqIO HOWTO
> Dear Dr. Moore,
> Thank you very much.
> You are right. The script works correctly only if the
> input is in genbank format but not the fasta format.
> One more question: I guess the read-in sequence is a
> string but not an array, am I right?
> Li
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