Stone::GB_Sequence(3) User Contributed Perl DocumentationStone::GB_Sequence(3)NAMEStone::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);
}
}
DESCRIPTIONStone::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
perl v5.14.1 2001-12-28 Stone::GB_Sequence(3)
