/localizaTE-v2.0

Pipeline for TE annotation in genome assemblies

Primary LanguagePerl

Install requirements

$ sudo pip install -r requirements.txt

Launch localizaTE-v2

  1. Edit config.py
  2. Launch LTR
  3. Launch Rmodeler
  4. Create Consensues
  5. Launch Pastec
  6. Launch RepeatMasker
  7. Get Statistics
  8. Obtain anotation in gff format
  9. Reconstruct fragments

1. Edit config.py

declare -rx localizaTEpath=#Path to localizaTe
declare -rx projectPath=#path to project
declare -rx projectName=pleostest
declare -rx projectFile=$projectName.fa

. $localizaTEpath/setEnv.sh

2. Launch LTR

# Start Interactive session
srun --pty bash -i
# srun --x11 --mem=6gb --cpus-per-task 8 --ntasks 1 --time 3:00:00 --pty bash -i
# exit --> exit from interactive session

touch nohup.out && nohup python $localizaTEpath/launchLTRpipeline.py $projectFile &

3. Launch runRModeler

python $localizaTEpath/launchRmodeler.py $projectFile

4. Create Consensues

# in Project folder: et:20 sec
bash $localizaTEpath/bin/create_consensus.sh RM_10649.TueApr181106352017 &

5. Launch PASTEC

# in library folder: et:100 sec
bash $localizaTEpath/bin/prepare_pastec.sh
#adapt configfile and run PASTEC (project name and project dir)
# renamee cleanlibrary.fa --> projectName.fa
# et 10'
nohup PASTEClassifier.py -i $projectFile -C PASTEClassifier_parallelized.cfg -p &

#get classified library:
# Manually revise the "unknown_elements.txt" file to be sure nothing is left and obtain final library, including reference fungal ClassII elements

python $localizaTEpath/bin/GetclassifiedLibrary.py cleanlibrary.fa $projectName.classif
python $localizaTEpath/bin/create_final_lib.py $projectName

# ...* renamed.fa: Libraries with their own seqs, with aliasname included
# ...* _locTE_v2_RefSeq.fa: Final libraries with elements from *renamed + ClassII
# Final libraries: $projectPath/FINAL/

6. Launch RepeatMasker

sbatch -p intel $localizaTEpath/bin/run_repeatmasker.sh \
$projectPath/pleostest.fa \
$projectPath/FINAL/classified_library_renamed.fa_locTE_v2_RefSeq.fa \
pleostest


RepeatMasker -pa 12 -s -e ncbi -frag 40000 -gff -lib $projectPath/FINAL/classified_library_renamed.fa_locTE_v2_RefSeq.fa $projectPath/pleostest.fa