Raw content of Bio::EnsEMBL::Analysis::Config::GeneBuild::ExamineGeneSets
<![CDATA[#
# Ensembl configuration file used in
#
# Bio::EnsEMBL::Analysis::RunnableDB::OrthologueEvaluator
#
# Copyright (c) 2006 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::Config::GeneBuild::OrthologueEvaluator
=head1 SYNOPSIS
Bio::EnsEMBL::Analysis::Config::GeneBuild::OrthologueEvaluator
=head1 DESCRIPTION
OrthologueEvaluator - Configuration
This is the main configuration file for OrthologueEvaluator, a perl
module which uses information from an Ensembl Compara database to
compare and assess gene predictions.
The parameters to connect to various databases are defiend in
- modules/Bio/EnsEMBL/Analysis/Config/GeneBuild/Databases.pm
- modules/Bio/EnsEMBL/Analysis/Config/OrthologueEvaluator.pm
The general function of this config file is to import a number of
standard global variables into the calling package. Without arguments
all the standard variables are set, and with a list, only those variables
whose names are provided are set. The module will die if a variable
which doesn\'t appear in its C<%Config> hash is asked to be set.
The variables can also be references to arrays or hashes.
Edit C<%Config> to add or alter variables.
All the variables are in capitals, so that they resemble environment
variables.
=head1 CONTACT
B<ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::Analysis::Config::GeneBuild::ExamineGeneSets;
use strict;
use vars qw(%Config);
%Config=
(
#
# GENE_DBNAME points to the DB of the species to investigate - this DB
# should be the same as the one which was used to do the compara run
# and is defined in Analysis/Config/Genebuild/Databases.pm
#
GENE_DBNAME => "REFERENCE_DB" ,
# GENE_DBNAME => "ORTHOLOGUES_DB" ,
# databases where to write recovered genes to ( connection details are defined in Databases.pm)
# if DO_NOT_READ_THE_EXONERATE2GENES_CONFIG_FILE == 1 the Exonerate2Genes.pm config file will be
# ignored (not read ) and the default parameters (hard-coded in the RunnableDB ) will be used
# to run Exonerat2Genes will be used. Nevertheless, you have to provide GENOMIC_SEQ and OUT_DBNAME
# if you decide to use the E2G config these settings will be ignored !
DO_NOT_READ_THE_EXONERATE2GENES_CONFIG_FILE => 1,
# this should point to dir || file where dumped genomic seq lives
GENOMIC_SEQ => "/data/blastdb/Ensembl/Dog/BROADD2/genome/softmasked_dusted/toplevel.fa",
# db where you want to write the results to ( should point to a db-connection in Databases.pm)
# ( you can also supply a hash-ref with the db-connection parameters if you like )
OUT_DBNAME => "ORTHOLOGUE_DB" ,
# do you want to run the exonerate jobs now or do you want to setup a post-analysis
# and upload the input ids ?
SETUP_POST_ANALYSIS___DO_NOT_RUN_EXONERATES_NOW => 0 ,
# the default can be found in Runnable/BaseExonerate.pm ( exonerate 0.8.3 )
EXONERATE_PROGRAM_FILE =>"/usr/local/ensembl/bin/exonerate-1.0.0",
# output-directory where we will write the files to
OUTPUT_DIR => "/lustre/scratch1/ensembl/jhv/patches/dog",
# WARNING !!!!! Only use the names out of the genome_db table in the compara databaase
SPECIES_TO_COMPARE => [ 'Mus musculus' , 'Homo sapiens'] ,
#
# S T A T I S T I C S
#
# this is for module FullStats.pm to plot exon/intron/cds/distributions
# of all genes in the databases no matter if there are orthologues or not
FULL_STATS_SPECIES => [ "Mus musculus","Homo sapiens"],
# if you want to limit the statistics-analysis to certain biotypes add them here -
# otherwise, all genes will be used
LIMIT_TO_GENE_BIOTYPES => ["protein_coding" ],
R_BINARY_LOCATION => "/vol/software/linux-x86_64/R-2.4.0/bin/R",
R_OUTPUT_DIR => "/lustre/work1/ensembl/jhv/project_genestructure_comparison/r_output",
#
# dir with old scripts :
# R_SCRIPTS_DIR => "/lustre/work1/ensembl/jhv/project_genestructure_comparison/rscripts_old/",
#
# new scripts are kept in cvs-personal
R_SCRIPTS_DIR => "/nfs/acari/jhv/cvs_checkout/ensembl-personal/jhv/projects/genestruc_comp/r_scripts",
# specify here the r-script you like to run ( it should be in the dir R_SCRITPTS_DIR,
# the data-file you want to use as input and, if your script writs output-files,
# specify the name of the output -file
R_ANALYSIS => {
# plot CDS-length per transcript and exons per transcript
"gt_analysis" => {
'r_script' => "exon_dist.R",
'data_file' => "full_exon_report.txt",
'ouput_file' => "",
'use_sweave' => 0,
},
# # plot CDS-length per transcript
# "cds_length_trans" => {
# 'r_script' => "trans_cds_length_stats.r",
# 'data_file' => "full_gene_trans_report.txt",
# 'use_sweave' =>1 ,
# 'sweave_script' => "trans_cds_length_stats.Snw",
# },
#
#
# # plot percentage of exons-per-transcript in genome
# "exon_per_trans" => {
# 'r_script' => "full_gene_trans_stats_relative.r",
# 'data_file' => "full_gene_trans_report.txt",
# 'use_sweave' =>1 ,
# 'sweave_script' => "full_gene_trans_stats_relative.Snw",
# },
},
);
sub import {
my ($callpack) = caller(0);
my $pack = shift;
my @vars = @_ ? @_ : keys(%Config);
return unless @vars;
eval "package $callpack; use vars qw("
. join(' ', map { '$'.$_ } @vars) . ")";
die $@ if $@;
foreach (@vars) {
if (defined $Config{ $_ }) {
no strict 'refs';
*{"${callpack}::$_"} = \$Config{ $_ };
} else {
die "Error: Config: $_ not known\n";
}
}
}
1;
]]>