Bio::Index SwissPfam
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Bio::Index::SwissPfam - Interface for indexing swisspfam files
Package variables
No package variables defined.
Included modules
    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; } } }
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, 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'.
No description
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 :
  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
    $VERSION = 0.1;
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;
sub _version {
    return $VERSION;
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
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.             - General discussion - 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:
AUTHOR - Ewan BirneyTop
Email -
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _