# File configuration for the user of Annocript
# READ CAREFULLY!!!
# This file has been written with a specific sintax. 
# The variables MUST stay in the format: variable = value
# A series of hashes (#########) closes the parameters to read
# Parameters of BLAST programs without a value assigned will not be used (i.e. word_sizeX = )
# When you want to execute something you have to write YES (in upper case) or NO otherwise
# other strings will give error.
##############################

#Allowed characters [A-za-z0-9\_\-]. Allowed extensions (fa|fasta). Please use a dot only to separate the extension! NB: reduced sequence name to just NCBI accession
fastaSeqs = Amel_RNA_shortNamesReal.fa

#organisms to blast ('all' means all the organisms in UniProt are taken)
#please use 'all' or a file name with organisms names
#Such file must be placed in your working directory (i.e. ann_works)
#Selection of the organisms works only if the TrEMBL database is used!
blastedOrganism = all

#How to extract GO terms: you can choose to extract 
#for proteins ('proteins'), domains ('domains') or for both ('both')
goTermsAss = both

#Steps to perform
doDbCreation = YES
doExecutePrograms = YES
doBuildOutput = YES
extractStatistics = YES

#Analyses to execute
doBlastxSP = YES
doBlastxTRorUf = YES
doRpstblastn = YES
doBlastn = YES
doPortrait = NO
doDna2Pep = YES

#Generation of a GFF database 
useGFFDB = YES
#Write YES, if you want GFF output files. Using NO increases the speed.)
printGFFOutput = YES

#BLASTX and BLASTP PARAMETERS (we use word_size 4 and threshold 18 to reduce computational time)
#(outfmt can be only 0 with this version of Annocript)
#Currently you can only use these parameters. Please ask in the forum if you need others.
word_sizeX = 4
evalueX = 1E-5
num_descriptionsX = 5
num_alignmentsX = 5
max_target_seqsX =
num_threadsX = 10
thresholdX = 18
matrixX = 

#BLASTN PARAMETERS
word_sizeN = 
evalueN = 0.00001
num_descriptionsN = 1
num_alignmentsN = 1
max_target_seqsN =
num_threadsN = 4
thresholdN =

#RPSBLAST and RPSTBLASTN PARAMETERS 
word_sizeRPS = 
evalueRPS = 0.00001
num_descriptionsRPS = 20
num_alignmentsRPS = 20
max_target_seqsRPS =
thresholdRPS =

#Number of threads for parallel executions (Used only for RPSBLAST)
threads4Parallel = 10

#BLAST results with evalue lower than evalMax will be shown in the tabular output
evalMax = 0.00001

#DNA2PEP PARAMETERS
d2pMode = none

#PLOTS
#Number of top scored elements to show in the plots (maximum is 50)
topToShow = 20
#Type of plot to show [currently you can use only barplot]
plotType = barplot

#Thresholds to be non-coding. They guide the heuristic in Annocript
#Minimum Portrait score
NCThresh = 0.95
#Maximum length of the ORF
NCORFLength = 100
#Minimum length of the transcript
NCSeqLength = 200

#FIXED PARAMETERS (You should set only once)#

#Database account info #Put your details in here
mySqlUser = something
mySqlPass = something

#UNIPROT informations for access #Put your details in here
uniprotWebUser = anonymous
uniprotWebPass = something@something.com

#Programs Paths #Put your details in here
blastPath = /path/to/blast/
portraitPath = /path/to/portrait-1.1.pl
dna2pepPath = /path/to/dna2pep.py
##############################