Stone::GB_Sequence

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 AT cshl DOT 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