Bio::Tools::Spidey::Results(3pm) | User Contributed Perl Documentation | Bio::Tools::Spidey::Results(3pm) |
Bio::Tools::Spidey::Results - Results of a Spidey run
use Bio::Tools::Spidey::Results; my $spidey = Bio::Tools::Spidey::Results->new(-file => 'result.spidey' ); # or my $spidey = Bio::Tools::Spidey::Results->new( -fh => \*INPUT ); # get the exons before doing anything else my $exonset = $spidey->next_exonset(); # parse the results my @exons = $exonset->sub_SeqFeature(); print "Total no of Exons: ", scalar(@exons), "\n"; print "Genomic sequence length: ", $spidey->genomic_dna_length(), "\n"; # $exonset is-a Bio::SeqFeature::Generic with Bio::Tools::Spidey::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) $spidey->close();
The spidey module provides a parser and results object for spidey output. The spidey results are specialised types of SeqFeatures, meaning you can add them to AnnSeq objects fine, and manipulate them in the "normal" seqfeature manner.
The spidey Exon objects are Bio::SeqFeature::FeaturePair inherited objects. The $esthit = $exon->est_hit() is the alignment as a feature on the matching object (normally, a cDNA), in which the start/end points are where the hit lies.
To make this module work sensibly you need to run
spidey -i genomic.fasta -m cDNA.fasta
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
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.
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
Email golharam@umdnj.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : $spidey->analysis_method(); Purpose : Inherited method. Overridden to ensure that the name matches /Spidey/i. Returns : String Argument : n/a
Title : parse_next_alignment Usage : @exons = $spidey_result->parse_next_alignment; foreach $exon (@exons) { # do something } Function: Parses the next alignment of the Spidey result file and returns the found exons as an array of Bio::Tools::Spidey::Exon objects. Call this method repeatedly until an empty array is returned to get the results for all alignments. Example : Returns : An array of Bio::Tools::Spidey::Exon objects Args :
Title : next_exonset Usage : $exonset = $spidey_result->parse_next_exonset; print "Exons start at ", $exonset->start(), "and end at ", $exonset->end(), "\n"; for $exon ($exonset->sub_SeqFeature()) { # do something } Function: Parses the next alignment of the Spidey 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::Spidey::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::Spidey::Exon objects as sub features. Args :
Title : next_feature Usage : while($exonset = $spidey->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 :
Title : genomic_dna_length Usage : $spidey->genomic_dna_length(); Function: Returns the length of the genomic DNA used in this Spidey result Example : Returns : An integer value. Args :
Title : splicesites Usage : $spidey->splicesites(); Function: Returns the number of splice sites found in this Spidey result Example : Returns : An integer value. Args :
Title : est_coverage Usage : $spidey->est_coverage(); Function: Returns the percent of est coverage in this Spidey result Example : Returns : An integer value. Args :
Title : overall_percentage_id Usage : $spidey->overall_percentage_id(); Function: Returns the overall percent id in this Spidey result Example : Returns : An float value. Args :
Title : missing_mrna_ends Usage : $spidey->missing_mrna_ends(); Function: Returns left/right/neither from Spidey Example : Returns : A string value. Args :
2018-10-27 | perl v5.26.2 |