get_5S_cov.sh

#!/bin/bash

if [ -z ${SLURM_CPUS_PER_TASK+x} ]; then
    cpus=32
else
    cpus=$SLURM_CPUS_PER_TASK
fi

SCRIPT_DIR=$1
fastq=$2
ref=$3
out_dir=$4
group=$(basename $fastq | cut -d. -f1)

echo $group 

prefix=$out_dir/alignment/5S/$group
temp_prefix=$out_dir/alignment/5S/temp/$group

# minimap2 \
#     -t $cpus \
#     -a \
#     -x map-ont \
#     -y \
#     --MD \
#     -Y \
#     $ref \
#     $fastq \
# | samtools sort -@$cpus -O BAM --write-index -o $temp_prefix.nofilter.bam##idx##$temp_prefix.nofilter.bam.bai -

# samtools view -@$cpus -F 260 -h -O BAM --write-index -o $temp_prefix.bam##idx##$temp_prefix.bam.bai $temp_prefix.nofilter.bam

# samtools view -@$cpus -h -O SAM -o $temp_prefix.sam $temp_prefix.bam 
# samtools view -@$cpus $temp_prefix.bam > $temp_prefix.no_header.sam
# samtools view -@$cpus -H $temp_prefix.bam > $temp_prefix.just_header.sam

# paftools.js sam2paf $temp_prefix.sam > $temp_prefix.paf

# python $SCRIPT_DIR/filter_both_18S.py $temp_prefix.no_header.sam $temp_prefix.paf sam 85 > $temp_prefix.filtered.sam
# python $SCRIPT_DIR/filter_both_18S.py $temp_prefix.no_header.sam $temp_prefix.paf paf 85 > $temp_prefix.filtered.paf

# awk '{print $1, $3, $4, $5}' $temp_prefix.filtered.paf > $temp_prefix.filtered.bed
# bash $SCRIPT_DIR/get_chimeras_for_python.sh $temp_prefix.filtered.bed > $temp_prefix.chimeras.txt

# if [[ $(cat $temp_prefix.chimeras.txt | wc -l) -eq 0 ]]; then
#     cp $temp_prefix.filtered.paf $prefix.paf
#     cp $temp_prefix.filtered.bed $prefix.bed
#     cat $temp_prefix.just_header.sam $temp_prefix.filtered.sam | samtools sort -@$cpus -O BAM --write-index -o $prefix.bam##idx##$prefix.bam.bai -
# else
#     python $SCRIPT_DIR/remove_chimeras.py $temp_prefix.filtered.paf $temp_prefix.chimeras.txt > $prefix.paf
#     python $SCRIPT_DIR/remove_chimeras.py $temp_prefix.filtered.bed $temp_prefix.chimeras.txt > $prefix.bed
#     cat $temp_prefix.just_header.sam $temp_prefix.filtered.sam > $temp_prefix.temp.sam
#     python $SCRIPT_DIR/remove_chimeras.py $temp_prefix.temp.sam $temp_prefix.chimeras.txt | samtools sort -@$cpus -O BAM --write-index -o $prefix.bam##idx##$prefix.bam.bai -
# fi

num_alns=$(cat $prefix.paf | wc -l)
echo -e "final alignments (reads to ref) $num_alns"

if [[ $num_alns -gt 0 ]]; then
    samtools depth \
        -@$cpus \
        -a \
        $prefix.bam \
        | awk '{sum+=$3} END {print sum/NR}' > $prefix.5S_cov.txt
fi