https://github.com/jdaeth274/ISA
Tip revision: c3873d851fdfb01efd8bb1f8a18f33acb06b6fc5 authored by jdaeth274 on 13 May 2021, 12:33:05 UTC
tweaking pbp blasting
tweaking pbp blasting
Tip revision: c3873d8
gps_rec_to_csv.pbs
#PBS -l select=1:ncpus=1:mem=2gb
#PBS -l walltime=01:00:00
#PBS -J 1-146
module load anaconda3/personal
source activate
conda activate insertion_site_analysis
cd /rds/general/project/bacterial_evo_genomics/live/gps_annotations_4_2_2020/gps_gubbins_runs
current_dir=$(head -n $PBS_ARRAY_INDEX dir_list.txt | tail -n 1)
cd $current_dir
out_prefix=$(echo $current_dir | grep -o -a gpsc\.[0-9]*_)
out_file="${out_prefix}recombinations.csv"
python ../ISA/python/embl_recombinations.py --embl_file *.recombination_predictions.embl \
--out_name $out_file
cd ../
echo $out_prefix >> embl_recombinations_csv_finished.txt