[Bioperl-l] All roads lead to Bio::Seq

[Viren Konde]

Yes, pretty easy to understand and Thanks.

-------------
Viren Konde, PhD
Postdoc, Univ. of Houston,
Dept. Biol. and Biochem.
TX 77204, USA.



Date: Tue, 03 Dec 2002 09:47:19 -0500
From: Lincoln Stein <lstein@cshl.org>
Subject: Re: [Bioperl-l] All roads lead to Bio::Seq
To: Ewan Birney <birney@ebi.ac.uk>,
bioperl-l@bioperl.org
Reply-to: lstein@cshl.org
Organization: Home

Looks good to me.

Lincoln

On Monday 02 December 2002 01:10 pm, Ewan Birney
wrote:
> I will soon commit this which is reorganise the
documentation in
> Bio::Seq, Bio::SeqI, Bio::PrimarySeqI and
Bio::PrimarySeq to stress
> that Bio::Seq has the best documentation and
starting point for users
> of the package. I am also using [Developers] in the
=head1 NAME line 
to
> indicate that a package is for developers only.
>
> I will commit this because I think this is much much
better than what 
is
> there at the moment, which was pretty confusing, but
recent-newbies - 
any
> other thoughts about this synopsis and also any
other reassuring 
words
> to make in Bio::Seq?
>
>
> Here is the Bio::Seq synopsis...
>
>
>
>     # This is the main sequence object in Bioperl
>
>     # gets a sequence from a file
>     $seqio  = Bio::SeqIO->new( '-format' => 'embl' ,
-file =>
> 'myfile.dat'); $seqobj = $seqio->next_seq();
>
>     # SeqIO can both read and write sequences; see
Bio::SeqIO
>     # for more information and examples
>
>     # get from database
>     $db = Bio::DB::GenBank->new();
>     $seqobj = $db->get_Seq_by_acc('X78121');
>
>     # make from strings in script
>     $seqobj = Bio::Seq->new( -display_id => 'my_id',
> 			     -seq => $sequence_as_string);
>
>     # gets sequence as a string from sequence object
>     $seqstr   = $seqobj->seq(); # actual sequence as
a string
>     $seqstr   = $seqobj->subseq(10,50); # slice in
biological 
coordinates
>
>     # retrieves information from the sequence
>     # features must implement Bio::SeqFeatureI
interface
>
>     @features = $seqobj->get_SeqFeatures(); # just
top level
>     foreach my $feat ( @features ) 
> 	print "Feature ",$feat->primary_tag," starts
",$feat->start," ends 
",
> 	$feat->end," strand ",$feat->strand,"\n";
>
>         # features retain link to underlying
sequence object
>         print "Feature sequence is
",$feat->seq->seq(),"\n"
>     
>
>     # sequences may have a species
>
>     if( defined $seq->species ) 
> 	print "Sequence is from ",$species->binomial_name,"
> [",$species->common_name,"]\n"; 
>
>     # annotation objects are
Bio::AnnotationCollectionI's
>     $ann      = $seqobj->annotation(); # annotation
object
>
>     # references is one type of annotations to get.
Also get
>     # comment and dblink. Look at
Bio::AnnotationCollection for
>     # more information
>
>     foreach my $ref (
$ann->get_Annotations('reference') ) 
> 	print "Reference ",$ref->title,"\n";
>     
>
>     # you can get truncations, translations and
reverse complements, 
these
>     # all give back Bio::Seq objects themselves,
though currently 
with no
>     # features transfered
>
>     my $trunc = $seqobj->trunc(100,200);
>     my $rev   = $seqobj->revcom();
>
>     # there are many options to translate
>     my $trans = $seqobj->translate();
>
>     # these functions can be chained together
>
>     my $trans_trunc_rev = 
$seqobj->trunc(100,200)->revcom->translate();
>
>
>
> _______________________________________________
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-- 
Lincoln Stein
lstein@cshl.org



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