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Bio::Tools::HMMER::ResUser(Contributed Perl DocumBio::Tools::HMMER::Results(3)

NAME
       Bio::Tools::HMMER::Results - Object representing	HMMER output results

SYNOPSIS
	  # parse a hmmsearch file (can	also parse a hmmpfam file)
	  $res = Bio::Tools::HMMER::Results->new( -file	=> 'output.hmm'	,
						 -type => 'hmmsearch');

	  # print out the results for each sequence
	  foreach $seq ( $res->each_Set	) {
	      print "Sequence bit score	is",$seq->bits,"\n";
	      foreach $domain (	$seq->each_Domain ) {
		  print	" Domain start ",$domain->start," end ",$domain->end,
		  " score ",$domain->bits,"\n";
	      }
	  }

	  # new	result object on a sequence/domain cutoff of
	  # 25 bits sequence, 15 bits domain
	  $newresult = $res->filter_on_cutoff(25,15);

	  # alternative	way of getting out all domains directly
	  foreach $domain ( $res->each_Domain )	{
	      print "Domain on ",$domain->seq_id," with	score ",
	      $domain->bits," evalue ",$domain->evalue,"\n";
	  }

DESCRIPTION
       This object represents HMMER output, either from	hmmsearch or hmmpfam.
       For hmmsearch, a	series of HMMER::Set objects are made, one for each
       sequence, which have the	the bits score for the object. For hmmpfam
       searches, only one Set object is	made.

       These objects come from the original HMMResults modules used internally
       in Pfam,	written	by Ewan	Birney.	Ewan then converted them to BioPerl
       objects in 1999.	That conversion	is meant to be backwardly compatible,
       but may not be (caveat emptor).

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 one
       of the Bioperl mailing lists.  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
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

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

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

CONTRIBUTORS
       Jason Stajich, jason-at-bioperl.org

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

   next_feature
	Title	: next_feature
	Usage	: while( my $feat = $res->next_feature ) { # do	something }
	Function: SeqAnalysisParserI implementing function
	Example	:
	Returns	: A Bio::SeqFeatureI compliant object, in this case,
		  each DomainUnit object, ie, flattening the Sequence
		  aspect of this.
	Args	: None

   number
	Title	: number
	Usage	: print	"There are ",$res->number," domains hit\n";
	Function: provides the number of domains in the	HMMER report

   seqfile
	Title	: seqfile
	Usage	: $obj->seqfile($newval)
	Function:
	Example	:
	Returns	: value	of seqfile
	Args	: newvalue (optional)

   hmmfile
	Title	: hmmfile
	Usage	: $obj->hmmfile($newval)
	Function:
	Example	:
	Returns	: value	of hmmfile
	Args	: newvalue (optional)

   add_Domain
	Title	: add_Domain
	Usage	: $res->add_Domain($unit)
	Function: adds a domain	to the results array. Mainly used internally.
	Args	: A Bio::Tools::HMMER::Domain

   each_Domain
	Title	: each_Domain
	Usage	: foreach $domain ( $res->each_Domain()	)
	Function: array	of Domain units	which are held in this report
	Returns	: array
	Args	: none

   domain_bits_cutoff_from_evalue
	Title	: domain_bits_cutoff_from_evalue
	Usage	: $cutoff = domain_bits_cutoff_from_evalue(0.01);
	Function: return a bits	cutoff from an evalue using the
		  scores here. Somewhat	interesting logic:
		   Find	the two	bit score which	straddle the evalue
		   if( 25 is between these two points) return 25
		   else	return the midpoint.

		  This logic tries to ensure that with large signal to
		  noise	separation one still has sensible 25 bit cutoff
	Returns	:
	Args	:

   write_FT_output
	Title	: write_FT_output
	Usage	: $res->write_FT_output(\*STDOUT,'DOMAIN')
	Function: writes feature table output ala swissprot
	Returns	:
	Args	:

   filter_on_cutoff
	Title	: filter_on_cutoff
	Usage	: $newresults =	$results->filter_on_cutoff(25,15);
	Function: Produces a new HMMER::Results	module which has
		  been trimmed at the cutoff.
	Returns	: a Bio::Tools::HMMER::Results module
	Args	: sequence cutoff and domain cutoff. in	bits score
		  if you want one cutoff, simply use same number both places

   write_ascii_out
	Title	: write_ascii_out
	Usage	: $res->write_ascii_out(\*STDOUT)
	Function: writes as
		  seq seq_start	seq_end	model-acc model_start model_end	model_name
	Returns	:
	Args	:

	 FIXME:	Now that we have no modelacc, this is probably a bad thing.

   write_GDF_bits
	Title	: write_GDF_bits
	Usage	: $res->write_GDF_bits(25,15,\*STDOUT)
	Function: writes GDF format with a sequence,domain threshold
	Returns	:
	Args	:

   add_Set
	Title	: add_Set
	Usage	: Mainly internal function
	Function:
	Returns	:
	Args	:

   each_Set
	Title	: each_Set
	Usage	:
	Function:
	Returns	:
	Args	:

   get_Set
	Title	: get_Set
	Usage	: $set = $res->get_Set('sequence-name');
	Function: returns the Set for a	particular sequence
	Returns	: a HMMER::Set object
	Args	: name of the sequence

   _parse_hmmpfam
	Title	: _parse_hmmpfam
	Usage	: $res->_parse_hmmpfam($filehandle)
	Function:
	Returns	:
	Args	:

   _parse_hmmsearch
	Title	: _parse_hmmsearch
	Usage	: $res->_parse_hmmsearch($filehandle)
	Function:
	Returns	:
	Args	:

   parsetype
	Title	: parsetype
	Usage	: $obj->parsetype($newval)
	Function:
	Returns	: value	of parsetype
	Args	: newvalue (optional)

perl v5.24.1			  2017-07-08	 Bio::Tools::HMMER::Results(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | CONTRIBUTORS | APPENDIX

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