NAME

Bio::ToolBox - Tools for querying and analysis of genomic data

DESCRIPTION

These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them.

• Opening and saving common tab-delimited text formats

• Support for BED, GFF, VCF, narrowPeak files

• Scoring intervals with datasets from microarray and sequencing

• ChIPSeq, RNASeq, microarray expression

• Support for Bam, BigWig, BigBed, wig, and USeq data formats

• Intersection with other known annotation

• Works with any genomic annotation in GTF, GFF3, and UCSC formats

The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.

In many cases, working with genomic annotation in databases assumes the use of Bio::DB::SeqFeature::Store formatted databases, available with a number of different backend support, including SQLite, MySQL, and others.

SCRIPTS

The Bio::ToolBox comes complete with an entire suite of high quality scripts ready for a wide variety of analyses.

• Preparation of databases from public annotation sources

• Annotated feature collection and selection

• Data collection and scoring

• File format manipulation and conversion

• Some low-level processing of raw data

• Simple analysis and graphing of collected data

LIBRARIES

The libraries and modules are available to extend existing scripts or to write your own.

The primary module, which provides a convenient object-oriented interface for working with data files and collecting data. It is the one most users will want to work with.

The remaining modules are support and general modules. They are collections of exportable subroutines without a convenient object-oriented interface.

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 will be familiar to users of BioPerl, from which this module draws heavily.

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.

Bio::ToolBox::db_helper

This helper library interacts with databases, including a variety of BioPerl-style Bio::DB::* databases such as SeqFeature::Store, Bam, BigWig, BigBed, BigWigSet, and USeq. In most cases, unless specifically stated otherwise, most database functions assume the use of Bio::DB::SeqFeature::Store databases, particularly with regards to genomic annotation. The functions are fairly well abstracted, and the library will take care of handling the database specifics appropriately.

Bio::ToolBox::big_helper

This helper library takes care of converting text versions of wiggle, bedGraph, and Bed file formats into UCSC BigWig and BigBed formats.

EXAMPLE

The following is a simplified example of using the library to create a data collection script using an input file of gene identifiers (from a database) or a BED file of coordinates. The dataset could be a Bam, BigBed, BigWig, or USeq file of genomic data.

  use Bio::ToolBox::Data;
  
  my $file = $ARGV[0];
  my $dataset = $ARGV[1];
  unless ($file and $dataset) {
      die "usage: $0 <input_file> <dataset_file>\n";
  }
  
  ### Open a pre-existing file
  my $Data = Bio::ToolBox::Data->new(
        file    => $file,
  );
  
  ### Add new dataset column and metadata
  my $index = $Data->add_column('Data');
  $Data->metadata($index, 'dataset', $dataset);
  $Data->metadata($index, 'method', 'mean');
  $Data->metadata($index, 'stranded', 'sense');
  
  ### Iterate through the Data structure one row at a time
  my $stream = $Data->row_stream;
  while (my $row = $stream->next_row) {
          my $value = $row->get_score(
              dataset   => $dataset,
              method    => 'mean',
              stranded  => 'sense',
          );
          $row->value($index, $value);
  }
  
  ### write the data to file
  my $success = $Data->write_file();
  print "wrote file $success\n"; # file extension will be automatically changed 
  

The example illustrates the simplicity of opening an input file, automatically identifying the file format and necessary columns for establishing genomic intervals, automatically handling the genomic dataset file from which to collect the data, iterating through the table, collecting the score for each genomic interval from the dataset, and writing the changed table to a new file. Since the input format (BED file) is no longer proper, it will automatically change the extension and write a text file complete with metadata.

The script could easily be modified to add or alter functionality. For example, use a different method of combining scores for each interval, or restricting scoring to a fraction of the defined interval. For a fully-featured version of this data collection script, see the BioToolBox script get_datasets.pl.

REPOSITORY

Source code for the Bio::ToolBox package is maintained at https://github.com/tjparnell/biotoolbox/.

Bugs and issues should be submitted at https://github.com/tjparnell/biotoolbox/issues.

AUTHOR

 Timothy J. Parnell, PhD
 Dept of Oncological Sciences
 Huntsman Cancer Institute
 University of Utah
 Salt Lake City, UT, 84112

LICENSE

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.