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Bio-ToolBox-1.2
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/ Bio::ToolBox::db_helper::useq

NAME

Bio::ToolBox::db_helper::useq

DESCRIPTION

This module supports the use of useq file in the Bio::ToolBox distribution. Useq files are zip archives representing either intervals or scores. They may be used similarly to either bigWig or bigBed files. More information about useq files may be found at http://useq.sourceforge.net/useqArchiveFormat.html. USeq files use the extension .useq.

Scores from useq files may be collected using this module. Either a single score from an interval, or a hash of scores associated with positions across an interval.

Scores may be restricted to strand by specifying the desired strandedness. For example, to collect transcription data over a gene, pass the strandedness value 'sense'. If the strand of the region database object (representing the gene) matches the strand of the bed feature, then the data for that bed feature is collected.

USAGE

The module requires the Bio::DB::USeq package to be installed.

Load the module at the beginning of your program.

use Bio::ToolBox::db_helper::useq;

It will automatically export the name of the subroutines.

collect_useq_scores()

This subroutine will collect only the data values from a binary useq file for the specified database region. The positional information of the scores is not retained, and the values are best further processed through some statistical method (mean, median, etc.).

The subroutine is passed seven or more arguments in the following order:

1) The chromosome or seq_id
2) The start position of the segment to collect 
3) The stop or end position of the segment to collect 
4) The strand of the original feature (or region), -1, 0, or 1.
5) A scalar value representing the desired strandedness of the data 
   to be collected. Acceptable values include "sense", "antisense", 
   or "all". Only those scores which match the indicated 
   strandedness are collected.
6) The method or type of data collected. 
   Acceptable values include 'score', 'count' (returns the number 
   of features found), or 'length' (returns the lengths of the 
   features found).  
7) The paths to one or more USeq files. It's unlikely to collect 
   from more than one, but, hey, if you want to....

The subroutine returns an array of the defined dataset values found within the region of interest.

collect_useq_position_scores()

This subroutine will collect the score values from a binary useq file for the specified database region keyed by position.

The subroutine is passed the same arguments as collect_useq_scores().

The subroutine returns a hash of the defined dataset values found within the region of interest keyed by position. The feature midpoint is used as the key position. When multiple features are found at the same position, a simple mean (for score or length data methods) or sum (for count methods) is returned.

open_useq_db()

This subroutine will open a useq database connection. Pass the local path to a useq file (.useq extension). It will return the opened Bio::DB::USeq database object.

AUTHOR

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

This package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.