Bio::ToolBox

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Libraries

Several library modules are included in this distribution. The following is a brief description of the primary user-oriented libraries that are available. Links will take you to the full documentation on MetaCPAN.

• Bio::ToolBox::Data

  This is the primary library module for working with a table of data, either generated as a new list from a database of annotation, or opened from a tab-delimited text file, for example a BED file of regions. Columns and rows of data may be added, deleted, or manipulated with ease.

  Additionally, genomic data may be collected from a wide variety of sources using the information in the data table. For example, scoring microarray or sequencing data for each interval listed in the data table.

  This module uses an object-oriented interface. Many of the methods and API will be familiar to users of Bio::Perl.

• Bio::ToolBox::Data::Feature

  This is the object class for working with individual rows in a table of data. It provides a number of conventions for working with the rows in a standard fashion, for example returning the start column value regardless of which column it is or whether the table is bed or gff or an arbitrary text file. A number of convenience methods are present for collecting data from data files. This module is not used directly by the user, but its objects are returned when using Bio::ToolBox::Data iterators.

• Bio::ToolBox::Parser

  This is the base class for working with common annotation formats. By default, these will slurp an entire genomic annotation file into memory in a reasonably short amount of time, including parsing gene annotation into a nested, hierarchical structure. To minimize memory usage, the Bio::ToolBox::SeqFeature object class is used by default. There are three format-specific parsers.

  • Bio::ToolBox::Parser::bed

    This parses BED file and related formats, including BED files with 3-12 columns (BED3, BED6, BED12, and in between), bedGraph, narrowPeak, and broadPeak. For proper BED12 files, transcripts are parsed with child subfeatures including exon and CDS subfeatures.

  • Bio::ToolBox::Parser::gff

    This parses both GTF and GFF3 file formats. Unlike most other GFF parsers that work line-by-line only, this maintains parent and child hierarchical relationships as parent feature and child subfeatures. To further maintain control and reduce unnecessary parsing, unwanted feature types can be selectively skipped.

  • Bio::ToolBox::Parser::ucsc

    This parses various UCSC file formats, including different refFlat, GenePred, and knownGene flavors. Genes, transcripts, and exons are assembled into hierarchical child-parent relationships as desired.

• Bio::ToolBox::SeqFeature

  This is a fast, lean, simple object class for representing genomic features. It supports, for the most part, the Bio::SeqFreatureI and Bio::RangeI API interface without the dependencies. It uses an unorthodox blessed-array object structure, which provides measurable improvements in memory consumption and speed when loading thousands of annotated SeqFeature objects (think mm39 or hg38 annotation).

• Bio::ToolBox::GeneTools

  This is a collection of exportable functions for working with Bio::SeqFeatureI compliant objects representing genes and transcripts. It works with objects derived from one of the “Annotation parsers” or a Bio::DB::SeqFeature::Store database. The functions make hard things easy, such as identifying whether a transcript is coding or not (is it encoded in the primary_tag or source_tag or GFF attribute or does it have CDS subfeatures?), or identify the alternative exons or introns of a multi-transcript gene, or pull out the 5' UTR (which may not be explicitly defined in the table).