Provided by: libbio-perl-perl_1.6.901-2_all bug

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://redmine.open-bio.org/projects/bioperl/

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    :