NAME

get_intersecting_features.pl

A script to pull out overlapping features from the database.

SYNOPSIS

get_intersecting_features.pl [--options] <filename>

Options:
--in <filename>
--db <database>
--feature <text>
--start <integer>
--stop <integer>
--extend <integer>
--ref [start | mid]
--out <filename>
--gz
--version
--help

OPTIONS

The command line flags and descriptions:

--in <filename>

Specify the file name of a list of reference features to find overlapping target features. These reference features may be genomic coordinates (chromo, start, stop) or named features (name, type). A tim data formatted file is best used but other tab delimited text formats may be used.

--db <database>

Provide the name of a Bio::DB::SeqFeature store database to use when finding features. If not specified, the database specified in the input file metadata will be used.

--feature <text>

Specify the name of the target features to search for in the database that intersect with the list of reference features. The type may be a either a GFF "type" or a "type:method" string. If not specifed, then the database will be queried for potential GFF types and a list presented to the user to select one.

--start <integer>, --stop <integer>

Optionally specify the relative start and stop positions from the 5' end (or start coordinate for non-stranded features) with which to restrict the region when searching for target features. For example, specify "--start=-200 --stop=0" to restrict to the promoter region of genes. Both positions must be specified. Default is to take the entire region of the reference feature.

--extend <integer>

Optionally specify the number of bp to extend the reference feature's region on each side. Useful when you have small reference regions and you want to include a larger search region.

--ref [start | mid]

Indicate the reference point from which to calculate the distance between the reference and target features. The same reference point is used for both features. Valid options include "start" (or 5' end for stranded features) and "mid" (for midpoint). Default is "start".

--out <filename>

Optionally specify a new filename. A standard tim data text file is written. The default is to rewrite the input file.

--gz

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

--version

Print the version number.

--help

Display the POD documentation

DESCRIPTION

This program will take a list of reference features and identify target features which intersect them. The reference features may be either named features (name and type) or genomic regions (chromosome, start, stop). By default, the search region for each reference feature is the entire feature, but may be restricted or expanded in size with appropriate modifiers (--start, --stop, --extend). The target features are specifed as specific types.

Several attributes of the found features are appended to the original input file data. First, the number of target features are reported. If more than one are found, the feature with the most overlap with the reference feature is preferentially listed. The name, type, and strand of the selected target feature is reported. Finally, the distance from the reference feature to the target feature is reported. The reference points for measuring the distance is by default the start or 5' end of the features, or optionally the midpoints. Note that the distance measurement is relative to the coordinates after adjustment with the --start, --stop, and --extend options.

A standard tim data text file is written.

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.