/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Index::Hmmer

NAME

Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query

SYNOPSIS

# Complete Code for indexing a set of report files
#!/usr/bin/perl -w
use strict;
use Bio::Index::Hmmer;
my $indexfile = shift;
my $index = Bio::Index::Hmmer->new(
	-filename => $indexfile,
	-write_flag => 1
);
$index->make_index(@ARGV);


# Complete code for fetching a report
use strict;
use Bio::Index::Hmmer;
my $indexfile = shift;
my $index = Bio::Index::Hmmer->new(
	-filename => $indexfile,
	-write_flag => 0
);

foreach my $id (@ARGV) {
	my $report = $index->fetch_report($id);
	print "Query: ", $report->query_name(), "\n";
	while( my $hit = $report->next_hit() ) {
		print "\tHit Name: ", $hit->name(), "\n";
		while( my $hsp = $hit->next_domain() ) {
			print "\t\tE-Value: ", $hsp->evalue(), "\n";
		}
	}
}

DESCRIPTION

This object allows one to build an index on a HMMER file (or files) and provide quick access to the HMMER report for that accession. 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
$inx->make_index($file_name);

# here is where the retrieval key is specified
sub get_id {
   my $line = shift;
   $line =~ /^KW\s+([A-Z]+)/i;
   $1;
}

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

AUTHOR - Josh Lauricha

Email laurichj@bioinfo.ucr.edu

APPENDIX

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

new

Usage   : $index = Bio::Index::Hmmer->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.
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::Hmmer implemented methods

fetch_report

Title   : fetch_report
Usage   : my $report = $idx->fetch_report($id);
Function: Returns a Bio::Search::Result::HMMERResult report object
          for a specific HMMER report
Returns : Bio::Search::Result::HMMERResult
Args    : valid id

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 blast dbs. 
          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

Require methods from Bio::Index::Abstract

_index_file

Title   : _index_file
Usage   : $index->_index_file( $file_name, $i )
Function: Specialist function to index HMMER report file(s).
          Is provided with a filename and an integer
          by make_index in its SUPER class.
Example : 
Returns : 
Args    :

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 don't 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