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    :