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Man Pages


Manual Reference Pages  -  STONE::GB_SEQUENCE (3)

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NAME

Stone::GB_Sequence - Specialized Access to GenBank Records

CONTENTS

SYNOPSIS



  use Boulder::Genbank;  # No need to use Stone::GB_Sequence directly
  $gb = Boulder::Genbank->newFh qw(M57939 M28274 L36028);

  while ($entry = <$gb>) {
    print "Entrys 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.

CW$length = CW$entry->length

Get the length of the sequence.

CW$start = CW$entry->start

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

CW$end = CW$entry->end

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

CW@feature_list = CW$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 <B>-posB> and/or <B>-typeB> argument names, as shown below.
-pos Provide a position or range of positions which the feature must <B>overlapB>. 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.

CW$seqObj = CW$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! <B>The above document had some coding errors, which are explained below:B>
Around line 90: You forgot a ’=back’ before ’=head2’
Around line 95: =back without =over
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perl v5.20.3 STONE::GB_SEQUENCE (3) 2001-12-28

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