03_BigWig_metPlot.sh

#! /bin/bash
  
## Allocate resources
#SBATCH --time=8-00:00:00
#SBATCH --partition=gpu
#SBATCH --array=0-24
#SBATCH --mem=64G
#SBATCH –-cpus-per-task=4

## job metadata
#SBATCH --job-name="Build_BigWig"
#SBATCH --mail-user=ahrmad.annan@students.unibe.ch
#SBATCH --mail-type=end,fail

source ./varSettings.sh

i=$SLURM_ARRAY_TASK_ID
j=$SLURM_ARRAY_JOB_ID
nb_arr=$SLURM_ARRAY_TASK_MAX
let nb_job="${#barcodesOfInterest[@]}"

if [ "${i}" = 0 ]; then scancel --quiet ${j}_[${nb_job}-${nb_arr}]; else sleep 1;fi 

source ${CONDA_ACTIVATE} ${condaEnv}
lib=${barcodesOfInterest[${i}]}

# Move to scratch temp experiment folder
cd /scratch/TMP_Megalodon_${expName}/megalodon_results_${lib}

# Run Python sqlite DB extraction
python ${work_DIR}/03_BigWig_metPlot_helper.py ${lib} ${k}

# Build Wigs
chrom=(chrI chrII chrIII chrIV chrM chrV chrX)

echo Formatting WIGS...
for j in $(seq 7); do
	echo Formatting Chrom ${j}
	echo variableStep chrom=${chrom[${j}-1]} span=1 >> ${lib}.wig
	cat ${j}.txt >> ${lib}.wig
	echo variableStep chrom=${chrom[${j}-1]} span=1 >> ${lib}_w10.wig
	cat ${j}_w10.txt >> ${lib}_w10.wig
	rm ${j}.txt ${j}_w10.txt
done
echo Formatting WIGS Done.
echo Building BIGWIGs...

# Build BigWigs
fetchChromSizes ce11 > ce11.chrom.sizes
wigToBigWig ${lib}.wig ce11.chrom.sizes ${lib}.bw
wigToBigWig ${lib}_w10.wig ce11.chrom.sizes ${lib}_w10.bw
echo Building BIGWIGs Done.

echo Remove intermediary files...
# Remove intermediary files
rm ${lib}.wig ${lib}_w10.wig ce11.chrom.sizes

#Remove Copy files to output folder
# Copy files to output folder
cp *.bw *.pdf ${work_DIR}/output/.

conda deactivate