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draw_densities.hetero.sh
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draw_densities.hetero.sh
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#!/bin/bash
print_usage() {
echo "Creating files for genome vizualization."
echo "run script in bcftools_filtration folder"
}
while getopts '' flag; do
case "${flag}" in
*) print_usage
exit 1 ;;
esac
done
# paths
assembly="../../../../../assemblies/hic/"
# script
for file in *.SNPs.hetero.vcf; do
SAMPLE=$(echo $file | cut -d'.' -f 3);
echo "${file} is being processed ...";
python3 $TOOLS/MACE/scripts/draw_variant_window_densities.py -i ${file} -o $SAMPLE.snps.100kb.hetero --subplots_adjust_left 0.35 -l "Heterozygous SNPs for $SAMPLE" -w 100000 -s 100000 -a ${assembly}/*.whitelist -z ${assembly}/*.orderedlist --scaffold_syn_file ${assembly}/*.syn --syn_file_key_column 0 --syn_file_value_column 1 --colormap jet --hide_track_label --density_thresholds 0,0.1,0.5,1,1.5,2,2.5,3,3.5,4,4.5,5,5.5,6,6.5,7;
python3 $TOOLS/MACE/scripts/draw_variant_window_densities.py -i ${file} -o $SAMPLE.snps.1mb.hetero --subplots_adjust_left 0.35 -l "Heterozygous SNPs for $SAMPLE" -w 1000000 -s 1000000 -a ${assembly}/*.whitelist -z ${assembly}/*.orderedlist --scaffold_syn_file ${assembly}/*.syn --syn_file_key_column 0 --syn_file_value_column 1 --colormap jet --hide_track_label --density_thresholds 0,0.1,0.5,1,1.5,2,2.5,3,3.5,4,4.5,5,5.5,6,6.5,7;
done