Bio::Index Stockholm
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Package variables
No package variables defined.
Included modules
Bio::Index::Abstract Bio::Root::Root
    use strict;
use Bio::Index::Stockholm;
my ($indexfile,$file1,$file2,$query);
my $index = Bio::Index::Stockholm->new(-filename => $indexfile,
-write_flag => 1);
# get raw data stream starting at alignment position my $fh = $index->get_stream($query); # fetch individual alignment my $align = $index->fetch_aln($query); # alias for fetch_report my $align = $index->fetch_report($query); # same as above print "query is ", $align->display_id, "\n";
Indexes Stockholm format alignments such as those from Pfam and Rfam.
Returns raw stream data using the ID or a Bio::SimpleAlign object
(via Bio::AlignIO).
This module also allows for ID parsing using a callback:
# make the index
# here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /^>.+gi\|(\d+)/; $1; }
The indexer is capable of indexing based on multiple IDs passed back from the
callback; this is assuming of course all IDs are unique. The default is to use
the alignment ID provided for Rfam/Pfam output.
Note: for best results 'use strict'.
Methods description
_versioncode    nextTop
  Title   : _version
Usage : $type = $index->_version()
Function: Returns a string which identifes the version of an
index module. Used to permanently identify an index
file as having been created by a particular version
of the index module. Must be provided by the sub class
Example :
Returns :
Args : none
  Usage   : $index = Bio::Index::Abstract->new(
-filename => $dbm_file,
-write_flag => 0,
-dbm_package => 'DB_File',
-verbose => 0);
Function: Returns a new index object. If filename is specified, then open_dbm() is immediately called. Bio::Index::Abstract->new() will usually be called directly only when opening an existing index. Returns : A new index object Args : -filename The name of the dbm index file. -write_flag TRUE if write access to the dbm file is needed. -dbm_package The Perl dbm module to use for the index. -verbose Print debugging output to STDERR if TRUE.
 Title   : fetch_report
Usage : my $align = $idx->fetch_report($id);
Function: Returns a Bio::SimpleAlign object
for a specific alignment
Returns : Bio::SimpleAlign
Args : valid id
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index report file(s).
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
  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 : reference to CODE if called without arguments
Args : CODE
  Title   : default_id_parser
Usage : $id = default_id_parser($line)
Function: The default parser for
Returns : Array of specified ids
Args : a line string
Methods code
sub _version {
	return ${Bio::Root::Version::VERSION};
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
sub fetch_report {
	my ($self,$id) = @_;
	my $fh = $self->get_stream($id);
	my $report = Bio::AlignIO->new(-noclose => 1,
									-format => 'stockholm',
						            -fh => $fh);
	return $report->next_aln;
sub _index_file {
  my( $self,
      $file,  # File name
$i # Index-number of file being indexed
) = @_; my $begin = 0; my $id_parser = $self->id_parser; open my $STOCKHOLM, '<', $file or $self->throw("Can't open file for read : $file"); my %done_ids; while (<$STOCKHOLM>) { if ( /^#\sSTOCKHOLM/ ) { $begin = tell($STOCKHOLM) - length($_); } for my $id ( &$id_parser($_) ) { next if exists $done_ids{$id}; $self->add_record($id, $i, $begin) if $id; $done_ids{$id} = 1; } %done_ids = () if ( m{//} ); } close $STOCKHOLM; 1;
sub id_parser {
  my ($self,$code) = @_;

  if ($code) {
    $self->{'_id_parser'} = $code;
  return $self->{'_id_parser'} ||\& default_id_parser;
sub default_id_parser {
  my $line = shift;
  my %accs;
  if ( $line =~ /^#=GF AC\s+(\S+)/ ) {
  keys %accs;
General documentation
- allow using an alternative regex for indexing (for instance, the ID instead of AC)
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.                  - General discussion - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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
of the bugs and their resolution. Bug reports can be submitted via the
AUTHOR - Chris FieldsTop
Email cjfields-at-bioperl-dot-org
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Index::Stockholm implemented methodsTop
 Title   : fetch_aln
Usage : my $align = $idx->fetch_aln($id);
Function: Returns a Bio::SimpleAlign object
for a specific alignment
Returns : Bio::SimpleAlign
Args : valid id
Note : alias for fetch_report
Require methods from Bio::Index::AbstractTop
Bio::Index::Abstract methodsTop
 Title   : filename
Usage : $value = $self->filename();
Function: Gets or sets the name of the dbm index file.
Returns : The current value of filename
Args : Value of filename if setting, or none if
getting the value.
 Title   : write_flag
Usage : $value = $self->write_flag();
Function: Gets or sets the value of write_flag, which
is wether the dbm file should be opened with
write access.
Returns : The current value of write_flag (default 0)
Args : Value of write_flag if setting, or none if
getting the value.
 Usage   : $value = $self->dbm_package();
Function: Gets or sets the name of the Perl dbm module used. If the value is unset, then it returns the value of the package variable $USE_DBM_TYPE or if that is unset, then it chooses the best available dbm type, choosing 'DB_File' in preference to 'SDBM_File'. Bio::Abstract::Index may work with other dbm file types. Returns : The current value of dbm_package Args : Value of dbm_package if setting, or none if getting the value.
 Title   : get_stream
Usage : $stream = $index->get_stream( $id );
Function: Returns a file handle with the file pointer
at the approprite place
This provides for a way to get the actual file contents and not an object WARNING: you must parse the record deliminter *yourself*. Abstract wont do this for you So this code $fh = $index->get_stream($myid); while( <$fh> ) { # do something } will parse the entire file if you do not put in a last statement in, like while( <$fh> ) { /^\/\// && last; # end of record # do something } Returns : A filehandle object Args : string represents the accession number Notes : This method should not be used without forethought
  Usage   : $index->open_dbm()
Function: Opens the dbm file associated with the index
object. Write access is only given if explicitly
asked for by calling new(-write => 1) or having set
the write_flag(1) on the index object. The type of
dbm file opened is that returned by dbm_package().
The name of the file to be is opened is obtained by
calling the filename() method.
Example : $index->_open_dbm() Returns : 1 on success
  Title   : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
Example :
Returns :
Args :
  Title   : _file_handle
Usage : $fh = $index->_file_handle( INT )
Function: Returns an open filehandle for the file
index INT. On opening a new filehandle it
caches it in the @{$index->_filehandle} array.
If the requested filehandle is already open,
it simply returns it from the array.
Example : $fist_file_indexed = $index->_file_handle( 0 );
Returns : ref to a filehandle
Args : INT
  Title   : _file_count
Usage : $index->_file_count( INT )
Function: Used by the index building sub in a sub class to
track the number of files indexed. Sets or gets
the number of files indexed when called with or
without an argument.
Example :
Returns : INT
Args : INT
  Title   : add_record
Usage : $index->add_record( $id, @stuff );
Function: Calls pack_record on @stuff, and adds the result
of pack_record to the index database under key $id.
If $id is a reference to an array, then a new entry
is added under a key corresponding to each element
of the array.
Example : $index->add_record( $id, $fileNumber, $begin, $end )
Returns : TRUE on success or FALSE on failure
Args : ID LIST
  Title   : pack_record
Usage : $packed_string = $index->pack_record( LIST )
Function: Packs an array of scalars into a single string
joined by ASCII 034 (which is unlikely to be used
in any of the strings), and returns it.
Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end )
Returns : STRING or undef
Args : LIST
  Title   : unpack_record
Usage : $index->unpack_record( STRING )
Function: Splits the sting provided into an array,
splitting on ASCII 034.
Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} )
Returns : A 3 element ARRAY
Args : STRING containing ASCII 034
 Title   : DESTROY
Usage : Called automatically when index goes out of scope
Function: Closes connection to database and handles to
sequence files
Returns : NEVER
Args : NONE