# This is the configuration file for Clench_plugin and Clench2.0

# Set the level of detail in the results, options are S and All.
# All will include the terms that have 4 or more genes assigned to
# them and those that are deemed enriched. S will include only those 
# terms that are deemed enriched.

LevelOfDetail = All

# Options are Y and N. Set to Y for assigning a gene annotated with a term
# to all the parents of the term. 

MapToParents = Y

# Set the choice for conversion of fine level annotations to a custom
# coarse level. Options are YC, YT and N. YC = custom level specified
# by a slimterm file. YT = custom level set by TAIR and N = leave annotations
# as is.

ConvertToSlim = N

# Choose source of annotations, options are LocalFile,LocalGOFile,TAIR

AnnotationSource = TAIR

# If using a local source (GO format or TAIR) to search for annotations, 
# specify its location
# You can get this file from:
# ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/Genes/Gene_Ontology/
# REQUIRED if AnnotationSource as 'LocalFile' or 'LocalGOFile'

AnnotationSourceFile = C:/<PATH>/SamplesFiles_for_conf/ATH_GO.20040323.txt

# Choose source for getting promoter sequences, options are LocalFile,TAIR
# If in doubt use TAIR. Set to None to skip promoter analysis

PromoterSource = LocalFile

# If using a local source (FASTA format file) to search for sequences, 
# specify its location
# You can get this file from:
# ftp://tairpub:tairpub@ftp.arabidopsis.org/home/tair/Sequences/blast_datasets/
# REQUIRED if PromoterSource as 'LocalFile'

PromoterSourceFile = C:/<PATH>/SamplesFiles_for_conf/Upstream_1000_Sample

# If using TAIR as source, specify the type of seq. Options are At_upstream_1000,
# At_upstream_500, At_upstream_3000
# REQUIRED if PromoterSource is 'TAIR'
# Will not work if the BkgIdFile has more than 2000 ids in it.

PromoterType = At_upstream_1000

# Specify the location of a text file containing motifs in IUPAC symbols.
# format of the file:
# each line should contain a IUPAC sequence,tab,name for the motif
#
# e.g. TTGACY	WRKY
# See MotifListWithNames.txt for the format

MotifFile = C:/<PATH>/SamplesFiles_for_conf/MotifListWithNames.txt

# Specify the location of the slimterms file, containing a list of GO terms
# that you wish to consider as 'slim'. You can also input a file in GO file
# format and Clench will pick out all GO ids from the file (e.g. goslim_plant_clean.2003).
# REQUIRED is Custom conversion to slimterms is wanted.

SlimTerms = C:/<PATH>/SamplesFiles_for_conf/goslim_plant_clean.2003

# Specify the type of Slim mapping desired. Options are OnlyOne and Complete
# OnlyOne will map the fine level annotation to one and only one term in your
# SlimTerms file. Complete will map the fine level annotation to all the slim terms
# encountered (from your SlimTerms file) while traversing the path from the fine 
# level annotation to the root of GO. The default is Complete.
# If no Slimterm is found the original fine level annotation will be preserved

MappingType = Complete

# Number of simulations to perform while estimating the False Discovery rate
# and calculating simulation based p-values.

NumberOfSim = 50

# Specify the acceptable False discovery rate. An FDR of 0.3 means that 3 out
# of 10 categories can be false positives based on the number of simulations
# performed (decided by NumberOfSim).

FDRcutoff = 0.3

# Specify the type of adjustment to the p-values in order to control the FDR
# 'global' will reduce the p-value cutoff by the same amount for all categories
# to achieve a final FDR specified by the FDRcutoff. 'stepped' will reduce the
# p-value cutoffs separately for different categories depending on the number
# of genes assigned to each category and the FDR specific for a category with that
# many genes.

CorrectionType = stepped

# The location of the GO database. You can use a database on a remote machine
# like this: DBI:mysql:mygo:server.edu
# If you are affiliated to penn state email nigam@psu.edu, you might be able
# to use our go database.

mygo = DBI:mysql:mygo

# User name for that database
user = username

# Password for that database

password = password

# List of GO ids that you consider useless to include in results
# These have to be on one line DO NOT break the line.

IgnoreList = GO:0000004|GO:0008372|GO:0005554|GO:0003674|GO:0005575|GO:0007582|GO:0005622|GO:0008150|GO:0005737|GO:0005623|GO:0003673

# Provide a Tab delimited text file to associate Ids with a description
# in the output

DescriptionFile = C:/<PATH>/SamplesFiles_for_conf/IdToDescription.txt