NAME

PJ::Database::Root - Perl module for genomic annotations

SYNOPSIS

  This is a dummy module which contains NOTHING. It serves as a beacon for
  other Perl programs to find the path to genomic annotations.

  require PJ::Database::Root;
  my $path = $INC{'PJ/Database/Root.pm'};
  $path = s/Root.pm$//;
  $path2genome = $path . $genome_name;  # mm9, rn4, etc.

DESCRIPTION

Program such as region_analysis.pl requires genomic annotations to properly assign functions to regions generated from peak or differential site detection program such as diffReps.

The genomic annotations, such as coordinates of genebody, TSS, pericentromere are stored in text files. It is important for region_analysis.pl to find those files and perform operations on them.

The module PJ::Database::Root is simply an empty .pm file that does nothing. However, it is convenient to have this module so that its path can be extracted from %INC.

EXPORT

None by default.

SEE ALSO

PJ::Genome

Mailing list: https://groups.google.com/forum/#!forum/diffreps-discuss

Web site: https://code.google.com/p/diffreps/

AUTHOR

Li Shen, <shenli.sam@gmail.com>

COPYRIGHT AND LICENSE

Copyright (C) 2010-2013 by Li Shen

diffReps goes under GNU GPL v3: http://www.gnu.org/licenses/gpl.html