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Dungeon Crawl Reference: Stone Soup 0.4.1 Bug Fix release!
07-19-2008
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Stone::GB_Sequence(3pm) User Contributed Perl Documentation 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," "; @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 perl v5.10.1 2011-03-05 Stone::GB_Sequence(3pm)