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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupport
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/issuesAUTHOR - 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 idfetch_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_reportRequire 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 : CODEdefault_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 stringBio::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 forethoughtopen_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 : INTadd_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 LISTpack_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 : LISTunpack_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 034DESTROY
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