man Stone::GB_Sequence () - Specialized Access to GenBank Records

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 CW$entry refers to a previously-created Stone::GB_Sequence object. Get the length of the sequence. Get the start position of the sequence, currently always 1. Get the end position of the sequence, currently always the same as the length. 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. 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