Bio::Index Swissprot
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Summary
Bio::Index::Swissprot - Interface for indexing one or more
Swissprot files.
Package variables
No package variables defined.
Included modules
Bio::Seq
Inherit
Bio::Index::AbstractSeq
Synopsis
  # Make an index for one or more Swissprot files:
use Bio::Index::Swissprot; use strict; my $index_file_name = shift; my $inx = Bio::Index::Swissprot->new( -filename => $index_file_name, -write_flag => 1); $inx->make_index(@ARGV); # Print out several sequences present in the index in Genbank # format: use Bio::Index::Swissprot; use Bio::SeqIO; use strict; my $out = Bio::SeqIO->new( -format => 'genbank', -fh => \*STDOUT ); my $index_file_name = shift; my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns a Bio::Seq object $out->write_seq($seq); } # alternatively my ($id, $acc); my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc);
Description
By default the index that is created uses the AC and ID identifiers
as keys. This module inherits functions for managing dbm files from
Bio::Index::Abstract.pm, and provides the basic functionality
for indexing Swissprot files and retrieving Sequence objects from
them. For best results 'use strict'.
You can also set or customize the unique key used to retrieve by
writing your own function and calling the id_parser() method.
For example:
   $inx->id_parser(\&get_id);
# make the index
$inx->make_index($index_file_name);
# here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /^KW\s+([A-Z]+)/i; $1; }
Methods
_type_stamp
No description
Code
_version
No description
Code
_index_fileDescriptionCode
id_parserDescriptionCode
default_id_parserDescriptionCode
_file_formatDescriptionCode
Methods description
_index_filecode    nextTop
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index Swissprot format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parsercodeprevnextTop
  Title   : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string.
Returns \&default_id_parser (see below) if not
set. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE
default_id_parsercodeprevnextTop
  Title   : default_id_parser
Usage : $id = default_id_parser( $line )
Function: The default parser for Swissprot.pm
Returns $1 from applying the regexp /^ID\s*(\S+)/
or /^AC\s+([A-Z0-9]+)/ to the current line.
Returns : ID string
Args : a line string
_file_formatcodeprevnextTop
 Title   : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
Methods code
_type_stampdescriptionprevnextTop
sub _type_stamp {
	return '__Swissprot_FLAT__'; # What kind of index are we?
}
_versiondescriptionprevnextTop
sub _version {
	return 0.1;
}
_index_filedescriptionprevnextTop
sub _index_file {
	# $file is file name, $i is number of file being indexed
my( $self, $file, $i ) = @_; # Offset from start of file
my $begin = 0; my $id_parser = $self->id_parser; open my $SWISSPROT,'<',$file or $self->throw("Can't read file: $file"); my %done_ids; while (<$SWISSPROT>) { if (/^ID\s+\S+/) { $begin = tell($SWISSPROT) - length( $_ ); } for my $id (&$id_parser($_)) { next if exists $done_ids{$id}; $self->add_record($id, $i, $begin) if $id; $done_ids{$id} = 1; } if (m{//}) { %done_ids = (); } } close $SWISSPROT; return 1;
}
id_parserdescriptionprevnextTop
sub id_parser {
	my( $self, $code ) = @_;

	if ($code) {
		$self->{'_id_parser'} = $code;
	}
	return $self->{'_id_parser'} ||\& default_id_parser;
}
default_id_parserdescriptionprevnextTop
sub default_id_parser {
	my $line = shift;
	if ($line =~ /^ID\s*(\S+)/) {
		return $1;
	} 
	elsif ($line =~ /^AC\s+([A-Z0-9]+)/) {
		return $1;
	}
}
_file_formatdescriptionprevnextTop
sub _file_format {
   return 'swiss';
}

1;

__END__
}
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/projects/bioperl/
AUTHOR - Ewan BirneyTop
Also lorenz@ist.org, bosborne at alum.mit.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _