NAME

Bio::ViennaNGS::UCSC - Perl extension for easy UCSC Genome Browser integration.

SYNOPSIS

  use Bio::ViennaNGS::UCSC;

DESCRIPTION

ViennaNGS::UCSC is a Perl extension for managing routine tasks with the UCSC Genome Browser. It comes with a set of utilities that serve as reference implementation of the routines implemented in the library. All utilities are located in the 'scripts' folder. The main functionality is provided by the make_assembly_hub function.

EXPORT

Routines: make_assembly_hub, make_track_hub

Variables: none

make_assembly_hub()

Build assembly hubs for the UCSC genome browser. This function takes 4 parameters: 1. absolute path of input fasta file(e.g. /home/user/input.fa) 2. path to the ouput directory (e.g. /home/user/assemblyhubs/) 3. base URL where the output folder will be placed for upload to the UCSC genome browser (e.g. http://www.foo.com/folder/) 4. path for the log file (/home/user/logs/assemblyhubconstructionlog)

make_track_hub()

Build track hubs for the UCSC genome browser. This function takes 4 parameters: 1. chromosome id as used in existing ucsc assembly hub (e.g. chr1) 2. path to the ouput directory (e.g. /home/user/assemblyhubs/) 3. base URL where the output folder will be placed for upload to the UCSC genome browser (e.g. http://www.foo.com/folder/) 4. path for the log file (/home/user/logs/assemblyhubconstructionlog)

SEE ALSO

perldoc ViennaNGS perldoc ViennaNGS::AnnoC

AUTHORS

Michael Thomas Wolfinger, <michael@wolfinger.eu> Florian Eggenhofer, <florian.eggenhofer@univie.ac.at>

COPYRIGHT AND LICENSE

Copyright (C) 2014

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.16.3 or, at your option, any later version of Perl 5 you may have available.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.