NAME

db_setup.pl

A program to setup a SeqFeature::Store SQLite database from UCSC data

SYNOPSIS

db_setup.pl [--options...] <UCSC database>

  Options:
  -d --db <UCSC database>
  -p --path </path/to/store/database> 
  -t --table [refGene|ensGene|knownGene|xenoRefGene|all]
  -k --keep
  -V --verbose
  -v --version
  -h --help

OPTIONS

The command line flags and descriptions:

--db <UCSC database>

Provide the short UCSC database name for the species and version you want to use. See http://genome.ucsc.edu/FAQ/FAQreleases.html for a current list of available UCSC genomes. Examples include hg19, mm10, danRer7, sacCer3, etc.

--path </path/to/store/database>

Specify the optional path to store the SQLite database file. The default path is the ~/lib.

--table [refGene|ensGene|knownGene|xenoRefGene|all]

Provide one or more UCSC tables to load into the database. They may be specified as comma-delimited list (no spaces) or as separate, repeated arguments. The default is refGene, ensGene, and knownGene (if available).

--keep

Keep the downloaded UCSC tables and converted GFF3 files. Default is to delete them.

--verbose

Show realtime database loading progress.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will simplify the task of generating an annotation database. You provide the short name of the UCSC database for the species and genome version you are interested in, and the script will automatically download gene annotation and build a Bio::DB::SeqFeature::Store database for use with BioToolBox scripts.

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.