Bio::Index SwissPfam
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Index::SwissPfam - Interface for indexing swisspfam files
Package variables
No package variables defined.
Included modules
Bio::Index::Abstract
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 James Gilbert's Fasta system. Note: for
best results 'use strict'.
Methods
BEGIN 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
BEGINTop
BEGIN {
    $VERSION = 0.1;
}
_versiondescriptionprevnextTop
sub _version {
    return $VERSION;
}
_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 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"); }
}
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/MailList.shtml - About the mailing lists
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
email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Ewan BirneyTop
Email - birney@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _