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Bio::Tools::Sim4::ResuUser3Contributed Perl DocumeBio::Tools::Sim4::Results(3)

NAME
       Bio::Tools::Sim4::Results - Results of one Sim4 run

SYNOPSIS
	  # to preset the order	of EST and genomic file	as given on the	sim4
	  # command line:
	  my $sim4 = Bio::Tools::Sim4::Results->new(-file => 'result.sim4',
						    -estfirst => 1);
	  # to let the order be	determined automatically (by length comparison):
	  $sim4	= Bio::Tools::Sim4::Results->new( -file	=> 'sim4.results' );
	  # filehandle:
	  $sim4	= Bio::Tools::Sim4::Results->new( -fh	=> \*INPUT );

	  # parse the results
	  while(my $exonset = $sim4->next_exonset()) {
	      #	$exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Sim4::Exons
	      #	as sub features
	      print "Delimited on sequence ", $exonset->seq_id(),
		    "from ", $exonset->start(),	" to ",	$exonset->end(), "\n";
	      foreach my $exon ( $exonset->sub_SeqFeature() ) {
		 # $exon is-a Bio::SeqFeature::FeaturePair
		 print "Exon from ", $exon->start, " to	", $exon->end,
		       " on strand ", $exon->strand(), "\n";
		 # you can get out what	it matched using the est_hit attribute
		 my $homol = $exon->est_hit();
		 print "Matched	to sequence ", $homol->seq_id,
		       " at ", $homol->start," to ", $homol->end, "\n";
	     }
	  }

	  # essential if you gave a filename at	initialization (otherwise the file
	  # stays open)
	  $sim4->close();

DESCRIPTION
       The sim4	module provides	a parser and results object for	sim4 output.
       The sim4	results	are specialised	types of SeqFeatures, meaning you can
       add them	to AnnSeq objects fine,	and manipulate them in the "normal"
       seqfeature manner.

       The sim4	Exon objects are Bio::SeqFeature::FeaturePair inherited
       objects.	The $esthit = $exon->est_hit() is the alignment	as a feature
       on the matching object (normally, an EST), in which the start/end
       points are where	the hit	lies.

       To make this module work	sensibly you need to run

	    sim4 genomic.fasta est.database.fasta
       or
	    sim4 est.fasta genomic.database.fasta

       To get the sequence identifiers recorded	for the	first sequence,	too,
       use A=4 as output option	for sim4.

       One fiddle here is that there are only two real possibilities to	the
       matching	criteria: either one sequence needs reversing or not. Because
       of this,	it is impossible to tell whether the match is in the forward
       or reverse strand of the	genomic	DNA. We	solve this here	by assuming
       that the	genomic	DNA is always forward. As a consequence, the strand
       attribute of the	matching EST is	unknown, and the strand	attribute of
       the genomic DNA (i.e., the Exon object) will reflect the	direction of
       the hit.

       See the documentation of	parse_next_alignment() for abilities of	the
       parser to deal with the different output	format options of sim4.

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, Hilmar Lapp
       Ewan Birney <birney-at-sanger.ac.uk> Hilmar Lapp	<hlapp-at-gmx.net> or
       <hilmar.lapp-at-pharma.novartis.com>.

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

   analysis_method
	Usage	  : $sim4->analysis_method();
	Purpose	  : Inherited method. Overridden to ensure that	the name matches
		    /sim4/i.
	Returns	  : String
	Argument  : n/a

   parse_next_alignment
	Title	: parse_next_alignment
	Usage	: @exons = $sim4_result->parse_next_alignment;
		  foreach $exon	(@exons) {
		      #	do something
		  }
	Function: Parses the next alignment of the Sim4	result file and	returns	the
		  found	exons as an array of Bio::Tools::Sim4::Exon objects. Call
		  this method repeatedly until an empty	array is returned to get the
		  results for all alignments.

		  The $exon->seq_id() attribute	will be	set to the identifier of the
		  respective sequence for both sequences if A=4	was used in the	sim4
		  run, and otherwise for the second sequence only. If the output does
		  not contain the identifier, the filename stripped of path and
		  extension is used instead. In	addition, the full filename
		  will be recorded for both features ($exon inherits off
		  Bio::SeqFeature::SimilarityPair) as tag 'filename'. The length
		  is accessible	via the	seqlength() attribute of $exon->query()	and
		  $exon->est_hit().

		  Note that this method	is capable of dealing with outputs generated
		  with format 0,1,3, and 4 (via	the A=n	option to sim4). It
		  automatically	determines which of the	two sequences has been
		  reversed, and	adjusts	the coordinates	for that sequence. It will
		  also detect whether the EST sequence(s) were given as	first or as
		  second file to sim4, unless this has been specified at creation
		  time of the object.

	Example	:
	Returns	: An array of Bio::Tools::Sim4::Exon objects
	Args	:

   next_exonset
	Title	: next_exonset
	Usage	: $exonset = $sim4_result->parse_next_exonset;
		  print	"Exons start at	", $exonset->start(),
			"and end at ", $exonset->end(),	"\n";
		  foreach $exon	($exonset->sub_SeqFeature()) {
		      #	do something
		  }
	Function: Parses the next alignment of the Sim4	result file and	returns	the
		  set of exons as a container of features. The container is itself
		  a Bio::SeqFeature::Generic object, with the Bio::Tools::Sim4::Exon
		  objects as sub features. Start, end, and strand of the container
		  will represent the total region covered by the exons of this set.

		  See the documentation	of parse_next_alignment() for further
		  reference about parsing and how the information is stored.

	Example	:
	Returns	: An Bio::SeqFeature::Generic object holding Bio::Tools::Sim4::Exon
		  objects as sub features.
	Args	:

   next_feature
	Title	: next_feature
	Usage	: while($exonset = $sim4->next_feature()) {
			 # do something
		  }
	Function: Does the same	as L<next_exonset()>. See there	for documentation of
		  the functionality. Call this method repeatedly until FALSE is
		  returned.

		  The returned object is actually a SeqFeatureI	implementing object.
		  This method is required for classes implementing the
		  SeqAnalysisParserI interface,	and is merely an alias for
		  next_exonset() at present.

	Example	:
	Returns	: A Bio::SeqFeature::Generic object.
	Args	:

perl v5.24.1			  2017-07-08	  Bio::Tools::Sim4::Results(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney, Hilmar Lapp | APPENDIX

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