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peptide_generation.sh
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peptide_generation.sh
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#!/bin/bash
# Generate a unique run ID
run_id=$(date +"%Y%m%d%H%M%S")
# Generate output file for prints
output_file="$run_id.txt"
# Default verbose mode is false
generate_only=false
selection=true
npep=10
bootstrap=500
# Function to display the help message
show_help() {
echo "Usage: generate.sh [OPTIONS]"
echo "Options:"
echo " -g Enable generate-only mode"
echo " -s Enable selection-only mode"
echo " --npep x Set the number of peptides generated (default: 10)"
echo " --bootstrap y Set the number of bootstrap iterations (default: 500)"
echo " -h Show help"
echo ""
echo "Example:"
echo " generate.sh -v -g --npep 50 --bootstrap 1000"
echo ""
}
# Parse command-line options
while [[ $# -gt 0 ]]; do
case $1 in
-g)
generate_only=true
shift
;;
-s)
selection=false
shift
;;
--npep)
npep=$2
shift 2
;;
--bootstrap)
bootstrap=$2
shift 2
;;
-h)
show_help
exit 0
;;
*)
echo "Invalid option: $1" >&2
show_help
exit 1
;;
esac
done
# Activate conda environment
# conda activate env
# Shift the positional parameters to skip past the options
shift "$((OPTIND-1))"
if $selection; then
python generate_peptide.py $npep $bootstrap #> "$output_file"
# run Tango on generated file peptide see http://tango.crg.es/about.jsp
bash results/tango_results/generated_peptides_tango.sh
mv *_.txt results/tango_results
grep "AGG" results/tango_results/peptide_agregg.txt | awk '{gsub(/AGG|AMYLO|TURN|HELIX|HELAGG|BETA/,"\t",$0); print;}' > results/tango_results/reformated_aggregated_peptides.tsv
sed -i '1s/^/\tAGG\tAMYLO\tTURN\tHELIX\tHELAGG\tBETA\n/' results/tango_results/reformated_aggregated_peptides.tsv
echo ""
echo "Ran and reformatted Tango in vitro prediction"
echo ""
if $generate_only ; then
exit 1
fi
fi
read -e -p "Enter the path to Aggrescan results file: " input_aggrescan_path
# Check if the input file exists
if [ -f "$input_aggrescan_path" ]; then
python select_active.py $input_aggrescan_path results/tango_results/reformated_aggregated_peptides.tsv #> "$output_file" #check for python file name
else
echo "Input file not found: $input_aggrescan_path"
exit 1
fi