Bio::Tools::Spidey::Results(3pm) User Contributed Perl Documentation Bio::Tools::Spidey::Results(3pm)
NAME
Bio::Tools::Spidey::Results - Results of a Spidey run
SYNOPSIS
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), "
";
print "Genomic sequence length: ", $spidey->genomic_dna_length(), "
";
# $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(), "
";
foreach my $exon ( $exonset->sub_SeqFeature() ) {
# $exon is-a Bio::SeqFeature::FeaturePair
print "Exon from ", $exon->start, " to ", $exon->end,
" on strand ", $exon->strand(), "
";
# 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, "
";
}
# essential if you gave a filename at initialization (otherwise
# the file stays open)
$spidey->close();
DESCRIPTION
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
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 - Ryan Golhar
Email golharam@umdnj.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
analysis_method
Usage : $spidey->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/Spidey/i.
Returns : String
Argument : n/a
parse_next_alignment
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 :
next_exonset
Title : next_exonset
Usage : $exonset = $spidey_result->parse_next_exonset;
print "Exons start at ", $exonset->start(),
"and end at ", $exonset->end(), "
";
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 :
next_feature
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 :
genomic_dna_length
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 :
splicesites
Title : splicesites
Usage : $spidey->splicesites();
Function: Returns the number of splice sites found in this Spidey result
Example :
Returns : An integer value.
Args :
est_coverage
Title : est_coverage
Usage : $spidey->est_coverage();
Function: Returns the percent of est coverage in this Spidey result
Example :
Returns : An integer value.
Args :
overall_percentage_id
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 :
missing_mrna_ends
Title : missing_mrna_ends
Usage : $spidey->missing_mrna_ends();
Function: Returns left/right/neither from Spidey
Example :
Returns : A string value.
Args :
perl v5.14.2 2012-03-02 Bio::Tools::Spidey::Results(3pm)