Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Index::Stockholm - Indexes Stockholm format alignments (such as those from Pfam and
       Rfam.  Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO)

SYNOPSIS

           use strict;
           use Bio::Index::Stockholm;
           my ($indexfile,$file1,$file2,$query);
           my $index = Bio::Index::Stockholm->new(-filename => $indexfile,
                                                                 -write_flag => 1);
           $index->make_index($file1,$file2);

           # 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";

DESCRIPTION

       This object allows one to build an index for any file (or files) containing Stockholm
       alignment format (such as Rfam and Pfam) and provides quick access to the alignment based
       on the alignment ID.

       This also allows for ID parsing using a callback:

          $inx->id_parser(\&get_id);
          # make the index
          $inx->make_index($file_name);

          # 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'.

TODO

       - allow using an alternative regex for indexing (for instance, the ID instead of AC)

FEEDBACK

   Mailing Lists
       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.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       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 Bugs
       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 web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chris Fields

       Email cjfields-at-bioperl-dot-org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
         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.

   Bio::Index::Stockholm implemented methods
   fetch_report
        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

   fetch_aln
        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::Abstract
   _index_file
         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    :

   id_parser
         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.  Useful
                   for (for instance) specifying a different
                   parser for different flavours of IDs (for instance,
                   custom stockholm-formated files).
                   Returns \&default_id_parser (see below) if not
                   set. If you supply your own id_parser
                   subroutine, then it should expect a fasta
                   description line.  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_parser
         Title   : default_id_parser
         Usage   : $id = default_id_parser( $header )
         Function: The default Blast Query ID parser for Bio::Index::Blast.pm
                   Returns $1 from applying the regexp /^>\s*(\S+)/
                   to $header.
         Returns : ID string
         Args    : a header line string

   Bio::Index::Abstract methods
   filename
        Title   : filename
        Usage   : $value = $self->filename();
                  $self->filename($value);
        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.

   write_flag
        Title   : write_flag
        Usage   : $value = $self->write_flag();
                  $self->write_flag($value);
        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.

   dbm_package
        Usage   : $value = $self->dbm_package();
                  $self->dbm_package($value);

        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.

   get_stream
        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

   open_dbm
         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

   _version
         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

   _filename
         Title   : _filename
         Usage   : $index->_filename( FILE INT )
         Function: Indexes the file
         Example :
         Returns :
         Args    :

   _file_handle
         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

   _file_count
         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

   add_record
         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

   pack_record
         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

   unpack_record
         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

   DESTROY
        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