Bio::Index
Hmmer
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Summary
Bio::Index::Hmmer - indexes HMMER reports and supports retreival based on query
Package variables
No package variables defined.
Included modules
Inherit
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;
}
Methods
Methods description
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::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. |
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 |
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 |
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 |
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 : |
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 (@header, @data, $line);
my $fh = $self->get_stream($id);
my $pos = tell($fh);
seek($fh, 0, 0);
while($line = <$fh>) {
push @header, $line;
last if $line =~ /Query sequence:/o;
}
seek($fh, $pos, 0);
while(<$fh>) {
push @data, $_ if defined;
last if m{//}o;
}
my $rfh = new IO::String(join('', @header, @data));
my $report = Bio::SearchIO->new(
-noclose => 1,
-format => 'hmmer',
-fh => $rfh
);
return $report->next_result();
}
} | sub id_parser
{
my( $self, $code ) =@_;
if ($code) {
$self->{'_id_parser'} = $code;
}
return $self->{'_id_parser'} ||\& default_id_parser;} | sub default_id_parser
{
if ($_[0] =~ /^\s*(\S+)/) {
return $1;
} else {
return;
}} | sub _index_file
{ my($self, $file, $i) = @_;
my($begin);
open(my $HMMER, '<', $file) or $self->throw("cannot open file $file");
my $id;
my $indexpoint = 0;
while(<$HMMER>) {
if( /Query sequence: ([^\s]+)/o ) {
$indexpoint = tell($HMMER);
foreach my $id ($self->id_parser()->($1)) {
print "id is $id, begin is $indexpoint\n" if $self->verbose() > 0;
$self->add_record($id, $i, $indexpoint);
}
}
}
close $HMMER;
return 1;} | General documentation
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
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.
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 - Josh Lauricha | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::Index::Hmmer implemented methods | Top |
| Require methods from Bio::Index::Abstract | Top |
| Bio::Index::Abstract methods | Top |
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.
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.
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.
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
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