NAME

compare_subfeature_scores.pl

A script to compare the scores between one or more subfeatures.

SYNOPSIS

compare_subfeature_scores.pl --in <filename> --out <filename>

Options:
--in <filename>
--out <filename> 
--parent <index>
--subfeature <index>
--score <index>
--gz
--version
--help

OPTIONS

The command line flags and descriptions:

--in <filename>

Specify the input file. It should be a tab-delimited text file with headers. At least three columns must be present: the name of the parent (gene) feature, the name of subfeature (transcript) and the score. The file may be compressed with gzip.

--out <filename>

Specify the output filename.

--parent <index>

Optionally specify the index column for the parent or gene name. If not specified, the program will interactively present a list of columns to choose from.

--subfeature <index>

Optionally specify the index column for the subfeature or transcript name. If not specified, the program will interactively present a list of columns to choose from.

--score <index>

Optionally specify the index column for the score to compare. If not specified, the program will interactively present a list of columns to choose from.

--gz

Specify whether (or not) the output file should be compressed with gzip.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will compare the scores of all the subfeatures of a parent feature. For example, comparing RNA expression of all of the alternative transcripts from a gene. As input, it expects a tab-delimited text file with at least three columns: the name of the parent (e.g. gene) feature (not expected to be unique in the file), the name of the subfeature (e.g. transcript; must be unique with respect to each parent feature), and a score for each subfeature. Such a file may be generated using the biotoolbox script get_gene_regions.pl followed by get_datasets.pl.

The program will output a new file. Each line will represent one parent feature. The columns include the parent feature name, number of subfeatures, the minimum and maximum subfeature names and scores, and the range of scores.

AUTHOR

Timothy J. Parnell, PhD
Howard Hughes Medical Institute
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.