Reference

Bio::Index::Stockholm(3pm)

Interface for indexing Stockholm files

NAME

Bio::Index::Stockholm - Interface for indexing Stockholm files

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

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:

   $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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

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.
            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

default_id_parser

  Title   : default_id_parser
  Usage   : $id = default_id_parser($line)
  Function: The default parser for Stockholm.pm
  Returns : Array of specified ids
  Args    : a 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 whether 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 won't 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

History