Bio::Index SwissPfam
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Summary
Bio::Index::SwissPfam - Interface for indexing swisspfam files
Package variables
No package variables defined.
Included modules
Bio::Seq
Inherit
Bio::Index::Abstract
Synopsis
    use Bio::Index::SwissPfam;
use strict;
my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name, '-write_flag' => 'WRITE'); $inx->make_index(@ARGV); use Bio::Index::SwissPfam; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns stream while( <$seq> ) { if(/^>/) { print; last; } } }
Description
SwissPfam is one of the flat files released with Pfam. This modules
provides a way of indexing this module.
Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and
provides the basic funtionallity for indexing SwissPfam files. Only
retrieves FileStreams at the moment. Once we have something better
(ie, an object!), will use that. Heavily snaffled from Index::Fasta system of
James Gilbert. Note: for best results 'use strict'.
Methods
_type_stamp
No description
Code
_version
No description
Code
_index_fileDescriptionCode
fetchDescriptionCode
Methods description
_index_filecode    nextTop
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index swisspfam format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
fetchcodeprevnextTop
  Title   : fetch
Usage : $index->fetch( $id )
Function: Returns a Bio::Seq object from the index
Example : $seq = $index->fetch( 'dJ67B12' )
Returns : Bio::Seq object
Args : ID
Methods code
_type_stampdescriptionprevnextTop
sub _type_stamp {
    return '__SWISSPFAM_FLAT__'; # What kind of index are we?
}
_versiondescriptionprevnextTop
sub _version {
    return 0.1;
}
_index_filedescriptionprevnextTop
sub _index_file {
    my( $self,
        $file, # File name
$i # Index-number of file being indexed
) = @_; my( $begin, # Offset from start of file of the start
# of the last found record.
$end, # Offset from start of file of the end
# of the last found record.
$id, # ID of last found record.
$acc, # accession of last record. Also put into the index
$nid, $nacc, # new ids for the record just found
); $begin = 0; $end = 0; open my $SP, '<', $file or $self->throw("Can't open file for read : $file"); # Main indexing loop
while (<$SP>) { if (/^>(\S+)\s+\|=*\|\s+(\S+)/) { $nid = $1; $nacc = $2; my $new_begin = tell($SP) - length( $_ ); $end = $new_begin - 1; if( $id ) { $self->add_record($id, $i, $begin, $end); if( $acc ne $id ) { $self->add_record($acc, $i, $begin, $end); } } $begin = $new_begin; $id = $nid; $acc = $nacc; } } # Don't forget to add the last record
$end = tell($SP); $self->add_record($id, $i, $begin, $end) if $id; close $SP; return 1;
}
fetchdescriptionprevnextTop
sub fetch {
    my( $self, $id ) = @_;
    my $desc;
    my $db = $self->db();
    if (my $rec = $db->{ $id }) {
        my( @record );
        my ($file, $begin, $end) = $self->unpack_record( $rec );
        # Get the (possibly cached) filehandle
my $fh = $self->_file_handle( $file ); # move to start
seek($fh, $begin, 0); return $fh; } else { $self->throw("Unable to find a record for $id in SwissPfam flat file index"); } } 1;
}
General documentation
FEED_BACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/project/bioperl
AUTHOR - Ewan BirneyTop
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _