Bio::Tools::Sim4::Results - Results of one Sim4 run
$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"; } }
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.
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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:
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : each_ExonSet Usage : Function: Example : Returns : Args :
Title : add_ExonSet Usage : Function: Example : Returns : Args :
Title : _parse_file Usage : Function: Example : Returns : Args :
Title : _parse_fh Usage : Function: Example : Returns : Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.