-
Notifications
You must be signed in to change notification settings - Fork 20
/
director.sh
executable file
·20 lines (16 loc) · 1.19 KB
/
director.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
#!/bin/bash
# Usage: $ ./director.sh
# This script directs the usage of VIGA by making use of parallel
# It parallelises all different fasta files with target contigs and runs VIGA pipeline single threaded for each one of them
parallel ' name=$(basename {} | sed "s/\.fasta//g")
mkdir result/${name}
cp run-viga result/${name}
cp modifiers.txt result/${name}
cp ${name}.fasta result/${name}
cd result/${name}
./run-viga --input ${name}.fasta --diamonddb /data/databases/RefSeq_Viral_DIAMOND/refseq_viral_proteins.dmnd --blastdb /data/databases/RefSeq_Viral_BLAST/refseq_viral_proteins --rfamdb /data/databases/rfam/Rfam.cm --hmmerdb /data/databases/pvogs/pvogs.hmm --threads 1 --modifiers modifiers.txt
python ~/scripts/genbankfeature.py ${name}_annotated.gbk
perl ~/scripts/unmapvigaannotations3.pl ${name}.fasta ${name}_annotated.fasta ${name}_annotated.csv ${name}_annotated_rename.csv ${name}_annotated.protein.faa ${name}_annotated.protein_rename.faa
python ~/scripts/add_vq.py ${name}_annotated_rename.csv ~/scripts/ViralQuotient.txt ${name}_annotated_rename_vq.csv
python ~/scripts/converter.py -i ${name}_annotated_rename_vq.csv -o ${name}_annotated_rename_vq.json
' ::: $(ls *.fasta)