Bio::S...Handler(3pm)

💖 NAME 💖

Bio::SeqIO::game::featHandler — a class for handling feature elements ✨

(that's Bio::S...Handler(3pm) to the manpage system, straight out of the User Contributed Perl Documentation, iykyk 🫶)

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🌸 SYNOPSIS 🌸

okay so real talk: this module is not used directly. it's backstage, not the main act 💅

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🦋 DESCRIPTION 🦋

Bio::SeqIO::game::featHandler takes game XML <annotation> elements and converts them into flattened Bio::SeqFeature::Generic objects, which then get added to the sequence. that's the whole glow-up, no cap ✨

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is literally 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 responsive 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 so we can keep track of 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 - Sheldon McKay 👑

Email mckays@cshl.edu

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📚 APPENDIX 📚

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ 🙈

🎀 new

• Title: new
• Usage: my $featHandler = Bio::SeqIO::game::featHandler->new($seq, $seq_h, $ann_l)
• Function: creates an object to deal with sequence features
• Returns: a handler object
• Args:
  • $seq — a Bio::SeqI compliant object
  • $seq_h — ref. to a hash of other sequences associated with the main sequence (proteins, etc)
  • $ann_l — ref. to a list of annotations

🧬 add_source

• Title: add_source
• Usage: $featHandler->add_source($seq->length, \%tags);
• Function: creates a source feature
• Returns: a Bio::SeqFeature::Generic object
• Args: sequence length and a ref. to a hash of tag/value attributes

🔎 has_gene

• Title: has_gene
• Usage: my $gene = $self->_has_gene($gene, $gname, $id)
• Function: method to get/set the current gene feature
• Returns: a Bio::SeqFeature::Generic object (if there is a gene)
• Args: (optional)
  • $gene — an XML element for the annotation
  • $gname — gene name
  • $id — gene ID (not always the same as the name)

🙈 _has_CDS

• Title: _has_CDS
• Usage: my $cds = $self->_has_CDS
• Function: internal getter/setter for CDS features
• Returns: a Bio::SeqFeature::Generic transcript object (or nothing)
• Args: a Bio::SeqFeature::Generic transcript feature

✨ add_annotation

• Title: add_annotation
• Usage: $featHandler->add_annotation($seq, $type, $id, $tags, $feats)
• Function: converts a containment hierarchy into an ordered list of flat features
• Returns: nothing
• Args:
  • $seq — a Bio::SeqI compliant object
  • $type — the annotation type
  • $id — the anotation ID
  • $tags — ref. to a hash of tag/value attributes
  • $feats — ref to an array of Bio::SeqFeature::Generic objects

💅 _add_generic_annotation

• Title: _add_generic_annotation
• Usage: $self->_add_generic_annotation($seq, $type, $id, $tags, $feats)
• Function: an internal method to handle non-gene annotations
• Returns: nothing
• Args:
  • $seq — a Bio::SeqI compliant object
  • $type — the annotation type
  • $id — the anotation ID
  • $tags — ref. to a hash of tag/value attributes
  • $feats — ref to an array of Bio::SeqFeature::Generic objects

🎁 feature_set

• Title: feature_set
• Usage: push @feats, $featHandler->feature_set($id, $gname, $set, $anntype);
• Function: handles <feature_span> hierarchies (usually a transcript)
• Returns: a list of Bio::SeqFeature::Generic objects
• Args:
  • $id — ID of the feature set
  • $gname — name of the gene
  • $set — the <feature_set> object
  • $anntype — type of the parent annotation

🛠️ _build_feature_set

• Title: _build_feature_set
• Usage: $self->_build_feature_set($set, 1) # 1 flag means retain the exon as a subfeat
• Function: an internal method to process attributes and subfeats of a feature set
• Returns: nothing
• Args:
  • $set — a <feature_set> element
  • 1 — optional flag to retain exons as subfeats. Otherwise, they will be converted to sublocations of a parent CDS feature

🔥 _add_feature_span

• Title: _add_feature_span
• Usage: $self->_add_feature_span($el, 1)
• Function: an internal method to process <feature_span> elements
• Returns: nothing
• Args:
  • $el — a <feature_span> element
  • 1 — an optional flag to retain exons as subfeatures

🧚 _add_CDS

• Title: _add_CDS
• Usage: my $cds = $self->_add_CDS($transcript, $tags)
• Function: an internal method to create a CDS feature from a transcript feature
• Returns: a Bio::SeqFeature::Generic object
• Args:
  • $transcript — a Bio::SeqFeature::Generic object for a transcript
  • $tags — ref. to a hash of tag/value attributes

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and that's a wrap bestie 🎀 this page ships with perl v5.32.1, dated 2021-08-15 — go forth and annotate responsibly 💜