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Stone::GB_Sequence.3pm

NAME

Stone::GB_Sequence - Specialized Access to GenBank Records

SYNOPSIS

   use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
   $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028);
 
   while ($entry = <$gb>) {
     print "Entry's length is ",$entry->length,"\n";
     @cds   = $entry->match_features(-type=>'CDS');
     @exons = $entry->match_features(-type=>'Exon',-start=>100,-end=>300);
   }
 }
 
 

DESCRIPTION

Stone::GB_Sequence provides several specialized access methods to the various fields in a GenBank flat file record. You can return the sequence as a Bio::Seq object, or query the sequence for features that match positional or descriptional criteria that you provide.

CONSTRUCTORS

This class is not intended to be created directly, but via a Boulder::Genbank stream.

METHODS

In addition to the standard Stone methods and accessors, the following methods are provided. In the synopses, the variable $entry refers to a previously-created Stone::GB_Sequence object.

$length = $entry->length

Get the length of the sequence.

$start = $entry->start

Get the start position of the sequence, currently always ``1''.

$end = $entry->end

Get the end position of the sequence, currently always the same as the length.

@feature_list = $entry->features(-pos=>[50,450],-type=>['CDS','Exon'])

features() will search the entry feature list for those features that meet certain criteria. The criteria are specified using the -pos and/or -type argument names, as shown below.

-pos

Provide a position or range of positions which the feature must overlap. A single position is specified in this way:

    -pos => 1500;         # feature must overlap postion 1500
 
 

or a range of positions in this way:

    -pos => [1000,1500];  # 1000 to 1500 inclusive
 
 

If no criteria are provided, then features() returns all the features, and is equivalent to calling the Features() accessor.

-type, -types

Filter the list of features by type or a set of types. Matches are case-insensitive, so ``exon'', ``Exon'' and ``EXON'' are all equivalent. You may call with a single type as in:

    -type => 'Exon'
 
 

or with a list of types, as in

    -types => ['Exon','CDS']
 
 

The names ``-type'' and ``-types'' can be used interchangeably.

$seqObj = $entry->bioSeq;

Returns a Bio::Seq object from the Bioperl project. Dies with an error message unless the Bio::Seq module is installed.

AUTHOR

Lincoln D. Stein <lstein@cshl.org>.

COPYRIGHT

Copyright 1997-1999, Cold Spring Harbor Laboratory, Cold Spring Harbor NY. This module can be used and distributed on the same terms as Perl itself.

SEE ALSO

Boulder, <Boulder:Genbank>, Stone

POD ERRORS

Hey! The above document had some coding errors, which are explained below:

Around line 90:

You forgot a '=back' before '=head2'

Around line 95:

=back without =over