Script_exemple

# Input file    dbFraise_sample.txt
# NCBI Taxdump  telechargement fait le 2020-03-05
# Host genome   GCA_000511835.1_GenomeFraise.fa (2020-03-05)
# Entropy       2.5 et 0
# db name       dbFraise200309
# K size        18 et 22
# Threads/file  2/10

# pour installer NCBI esearch/entrez direct
# sudo apt install ncbi-entrez-direct

### Custome database ###

# path to folder
cd Downloads/DisCVR_Unix/DIsCVR_macOS

# Data Download
bash downloadDataAndRefSeq.sh ./dbFraise/dbFraise_sample.txt ./dbFraise/dbFraise_sample/

# Database Files Generation
# Reference Genome Library
java -cp ./bin customdatabase.GenomesLibrary \
      ./dbFraise/dbFraise_sample.txt dbFraise200309 \
      ./dbFraise/dbFraise_sample/RefSeq/
# Genere le fichier /dbFraise/dbFraise_sample/RefSeq/dbFraise200309_referenceGenomesLibrary ; doit etre copie dans customisedDB
cp ./dbFraise/dbFraise_sample/RefSeq/dbFraise200309_referenceGenomesLibrary \
      ./customisedDB/

# Virus k-mers database
# Data Filtering
mkdir ./dbFraise/dbFraise_sample/DataSeq_filtered
cp -r ./dbFraise/dbFraise_sample/DataSeq/* \
      ./dbFraise/dbFraise_sample/DataSeq_filtered
java -cp ./bin customdatabase.DataSequences \
      ./dbFraise/dbFraise_sample/DataSeq_filtered \
      ./dbFraise/dbFraise_sample/RefSeq/dbFraise200309_referenceGenomesLibrary \
      dbFraise200309

# k-mers database file
java -cp ./bin customdatabase.KmersDatabaseBuild \
      ./dbFraise/dbFraise_sample/DataSeq_filtered \
      ./dbFraise/GCA_000511835.1_GenomeFraise.fa \
      dbFraise200309_0 \
      18 \
      2 \
      0 \
      10

java –jar D:\DisCVR_Windows\DisCVR_CL.jar D:\D37733_Fraise 22 fastq D:\DisCVR_Windows\customisedDB\dbFraise200309_25_22 customisedDB 2.5

java –jar C:\Users\jodjo\Desktop\DisCVR_Windows\DisCVR_CL.jar C:\Users\jodjo\Desktop\DisCVR_data\EvalR_Fraise 22 fastq.gz C:\Users\jodjo\Desktop\DisCVR_Windows\customisedDB\dbFraise200309_25_22 customisedDB 2.5

java –jar C:\Users\jodjo\Desktop\DisCVR_Windows\DisCVR_CL.jar C:\Users\jodjo\Desktop\data 22 fastq C:\Users\jodjo\Desktop\DisCVR_Windows\customisedDB\dbFramboise200312_25_22 customisedDB 2.5