/ 
bioperl-0.6
/ Bio::Tools::Sim4::Results

NAME

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

SYNOPSIS

   $sim4 = Bio::Tools::Sim4->new( -file => 'sim4.results' );
   $sim4 = Bio::Tools::Sim4->new( -fh   => \*INPUT );
   
   # parse the results.

   foreach $exonset ( $sim4->each_ExonSet() ) {
      # $exonset is-a SeqFeature::Generic with Bio::Tools::Sim4::Exons as sub features
      print "Delimited on sequence from ", $exonset->start(), " to ", $exonset->end() "\n";
      foreach $exon ( $exonset->each_Exon() ) {
	  # $exon is-a SeqFeature::Generic 
	  print "Exon from ", $exon->start, " to ", $exon->end, "\n";
          
          # you can get out what it matched using the homol_SeqFeature attribute
          $homol = $exon->homol_SeqFeature;
          print "Matched to sequence", $homol->seqname, " at ", $homol->start, " to ", $homol->end, "\n";
      }
   }

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::Homol inherited objects. The $h = $exon->homol_SeqFeature() is the seqfeature on the matching object, 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

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. The exon objects have their strand attribute set to 0. However, the homol objects have their strand attribute set to 1 or -1, depending on whether it needs reverse complementing for this to work.

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.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email birney@sanger.ac.uk

Describe contact details here

APPENDIX

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

each_ExonSet

Title   : each_ExonSet
Usage   :
Function:
Example :
Returns : 
Args    :

add_ExonSet

Title   : add_ExonSet
Usage   :
Function:
Example :
Returns : 
Args    :

_parse_file

Title   : _parse_file
Usage   : 
Function:
Example :
Returns : 
Args    :

_parse_fh

Title   : _parse_fh
Usage   :
Function:
Example :
Returns : 
Args    :