NAME

get_features.pl

A script to collect features from a BioPerl SeqFeature::Store database.

SYNOPSIS

get_features.pl --db <text> [--options...]

  Options:
  --db <text>
  --feature <type | type:source>
  --all
  --sub
  --coord
  --start=<integer>
  --stop=<integer>
  --pos [ 5 | m | 3 | 53 ]
  --out <filename>
  --bed
  --gff 
  --gz
  --version
  --help

OPTIONS

The command line flags and descriptions:

--db <text>

Specify the name of a Bio::DB::SeqFeature::Store annotation database from which gene or feature annotation may be derived. A database is required for generating new data files with features. For more information about using annotation databases, see https://code.google.com/p/biotoolbox/wiki/WorkingWithDatabases.

--feature <type | type:source>

Optionally specify the type of the feature(s) to collect. The GFF primary_tag or primary_tag:source_tag should be specified. More than one feature may be specified at a time, either as a comma de-limited list or separate options. If not specified, then an interactive list will be presented to the user for selection.

--all

Optionally indicate that all features present in the database must be included. By default, certain features may be excluded based on parameters defined in the BioToolBox configuration file. See below for details.

--sub

Optionally include all subfeatures in the output. For example, transcript, CDS, and/or exon subfeatures of a gene.

--coord

When writing a standard format file, optionally include the chromosome, start, stop, and strand coordinates. These are automatically included when writing a BED or GFF format.

--start=<integer>

--stop=<integer>

Optionally specify adjustment values to adjust the reported start and end coordinates of the collected regions. A negative value is shifted upstream (towards the 5 prime end), and a positive value is shifted downstream (towards the 3 prime end). Adjustments are made relative to the indicated position (--pos option, below) based on the feature strand. Adjustments are ignored if a GFF file is written.

--pos [ 5 | m | 3 | 53 ]

Indicate the relative position from which both coordinate adjustments are made. Both start and stop adjustments may be made from the respective 5 prime, 3 prime, or middle position as dictated by the feature's strand value. Alternatively, specify '53' to indicate that the start adjustment adjusts the 5 prime end and the stop adjustment adjusts the 3 prime end. The default is '53'.

--out <filename>

Specify the output file name. Default is the joined list of features.

--bed

Optionally indicate that a 6-column BED format file should be written. Currently, 12-column BED formats with exon information is not supported (yet).

--gff

Optionally indicate that a GFF3 format file should be written. This option enables the database features to be written completely with all attributes. Coordinate adjustments are ignored.

--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 extract a list of features from a database and write them out to a file. Specifically, the requested features in a Bio::DB::SeqFeature::Store schema database are pulled and written as either a list of named features with or without coordinate information, a BED-style formatted file, or a GFF3-formatted file. The GFF option is essentially a database dump, as it enables a low-level option to write the features as original GFF3 lines complete with all attributes.

Features may be specified through their GFF type or primary_tag. They may be specified as a command-line option or selected interactively from a presented list. They may be restricted through two options defined in the BioToolBox configuration file, biotoolbox.cfg. These include a database-specific or default database option, "chromosome_exclude", which excludes features located on the listed chromosomes (such as the mitochondrial chromosome), and the "exclude_tags", which are attribute keys and values to be avoided. More information may be found in the configuration file itself.

COORDINATE ADJUSTMENTS

Coordinates of the features may be adjusted as desired. Adjustments may be made relative to either the 5 prime, 3 prime, both ends, or the feature midpoint. Positions are based on the feature strand. Use the following examples as a guide.

upstream 500 bp only

  get_features.pl --start=-500 --stop=-1 --pos 5

1 kb total around 5 prime end

  get_features.pl --start=-500 --stop=500 --pos 5

last 500 bp of feature

  get_features.pl --start=-500 --pos 3

middle 500 bp of feature

  get_features.pl --start=-250 --stop=250 --pos m

entire feature plus 1 kb of flanking

  get_features.pl --start=-1000 --stop=1000 --pos 53

Note that positions are always in base coordinates, and the resulting regions may be 1 bp longer depending on whether the reference base was included or not.

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 Artistic License 2.0.