-
Notifications
You must be signed in to change notification settings - Fork 0
/
01.DeNovo_Mining.sh
51 lines (39 loc) · 1.71 KB
/
01.DeNovo_Mining.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#!bin/bash
#Script to run all de-novo TE mining softwares (RepeatModeler2, MITE Tracker and HelitronScanner)
Path_Genome="$1"
Genome_database_name="$2"
N_of_cores="$3"
Path_MITEs_tracker="$4" #Path MITE_tracker python installation
Path_HelitronScanner="$5" #Path Helitronscanner installation
eval "$(conda shell.bash hook)"
varGenome=$( echo "$1" | rev | cut -d "/" -f1 | rev )
mkdir RepeatModeler
mkdir MITEs
mkdir Helitrons
###################################RepeatModeler##################################################
pathMaster=$(pwd)
conda activate Repeats
cd ./RepeatModeler
ln -s "$1"
#Path to NINJA installation. Necessary for LTR pipeline of RepeatModeler
NINJA_DIR=/home/jacopomartelossi/.conda/envs/Repeats/bin
BuildDatabase -name "$2" -engine ncbi "$varGenome"
RepeatModeler -pa "$3" -engine ncbi -database "$2" -LTRStruct -debug 2>&1 | tee LTR_struct.log
cd ..
###################################MITEs Tracker###################################################
conda deactivate
conda activate MITE_tracker
cd ./MITEs
varMITEs=$(pwd)
cd "$4"
ln -s "$1"
python3 MITETracker.py -g "$varGenome" -j "$2"_MITEs -w "$3"
mv ./Results/"$2"_MITEs "$varMITEs"
cd "$pathMaster"
####################################Helitron Scanner##############################################
cd Helitrons
ln -s "$1"
java -jar "$5"/HelitronScanner.jar scanHead -lf "$5"/TrainingSet/head.lcvs -g "$varGenome" -bs 1000000 -o "$2".head
java -jar "$5"/HelitronScanner.jar scanTail -lf "$5"/TrainingSet/tail.lcvs -g "$varGenome" -bs 1000000 -o "$2".tail
java -jar "$5"/HelitronScanner.jar pairends -hs "$2".head -ts "$2".tail -o "$2".pairends -ht 10 -tt 10
java -jar "$5"/HelitronScanner.jar draw -g "$varGenome" -p "$2".pairends -o "$2".fasta --pure