Bio::T...Results(3pm)

💅 Bio::Tools::Spidey::Results ✨

okay so bestie, you've landed on the Bio::T...Results(3pm) page — yes that's the truncated glow-up of Bio::Tools::Spidey::Results(3pm) — and it's straight out of User Contributed Perl Documentation. Pull up a chair, this one's a whole vibe. 🦋

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✨ NAME ✨

Bio::Tools::Spidey::Results — it's the results of a Spidey run. That's the whole job description, and it ate. 💖

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🌸 SYNOPSIS 🌸

okay so here's the whole flow, no cap:

          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();

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🎀 DESCRIPTION 🎀

so the spidey module hands you a parser and a results object for spidey output. And here's the iconic part: the spidey results are specialised types of SeqFeatures, which literally means you can drop them into AnnSeq objects no problem and mess with them in the totally "normal" seqfeature manner. main character behaviour fr. 💅

the spidey Exon objects are Bio::SeqFeature::FeaturePair inherited objects, iykyk. and $esthit = $exon->est_hit() is the alignment as a feature on the matching object (normally, a cDNA), where the start/end points are where the hit lies. 🧬

and to make this module work sensibly you need to run:

     spidey -i genomic.fasta -m cDNA.fasta

periodt.

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely. send your comments and suggestions preferably to one of the Bioperl mailing lists, and 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. there are so many experienced and responsive experts who will be able look at the problem and quickly address it. 🙏 and bestie, please include a thorough description of the problem with code and data examples if at all possible. the more deets the better.

🐛 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

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👑 AUTHOR - Ryan Golhar 👑

Email golharam@umdnj.edu

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _, just so you know which ones are the backstage crew. 🌟

⭐ 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(), "\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 :

⭐ 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 :

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and that's the whole page bestie, you're officially a Spidey results expert 🧚💜 this one's running on perl v5.32.1 and it was last touched on 2021-08-15 — so go forth, parse some exons, and slay 💅✨