Make the MDMParis defense finder models compatible with Anvi'o.

gistfile1.txt

#!/bin/bash

# Set the GitHub repository and destination folder
github_repo="mdmparis/defense-finder-models"
destination_folder="DefenseFinder/"
source_folder="defense-finder-models"

# Function to check if a file exists, and exit with a warning if it does
check_file_exists() {
    if [ -e "$1" ]; then
        echo "Warning: File $1 already exists. Exiting."
        exit 1
    fi
}

# Function to download the latest release from GitHub
download_latest_release() {
    repo_url="https://api.github.com/repos/$1/releases/latest"
    download_url=$(curl -s "$repo_url" | grep "browser_download_url" | cut -d '"' -f 4)
    wget -O latest_release.tar.gz "$download_url"
    tar -xzf latest_release.tar.gz
    rm latest_release.tar.gz
}

# Check if any of the required files already exist
check_file_exists "$destination_folder/genes.hmm"
check_file_exists "$destination_folder/kind.txt"
check_file_exists "$destination_folder/reference.txt"
check_file_exists "$destination_folder/target.txt"
check_file_exists "$destination_folder/noise_cutoff_terms.txt"
check_file_exists "$destination_folder/genes.txt"

# Download the latest release from GitHub
download_latest_release "$github_repo"

# Create the destination folder if it doesn't exist
mkdir -p "$destination_folder"

# Create kind.txt with "DefenseFinder"
echo "DefenseFinder" > "$destination_folder/kind.txt"

# Extract version number from metadata.yml
version_number=$(grep "vers" "$source_folder/metadata.yml" | cut -d ' ' -f2)

# Create reference.txt with "DefenseFinder" and version number
echo "DefenseFinder $version_number" > "$destination_folder/reference.txt"

# Create target.txt with "AA:GENE"
echo "AA:GENE" > "$destination_folder/target.txt"

# Create noise_cutoff_terms.txt with "-E 1e-25"
echo "-E 1e-25" > "$destination_folder/noise_cutoff_terms.txt"

# Create genes.txt with "gene   accession   hmmsource"
echo -e "gene\taccession\thmmsource" > "$destination_folder/genes.txt"
for file in "$source_folder/profiles"/*.hmm; do
    base_name=$(basename "$file" .hmm)

    # Extract gene names and count occurrences within the file
    gene_counts=$(awk '/^NAME/ {if (++count[$2] == 1) print $2; else print $2"_"count[$2]}' "$file")

    # Loop through each gene name and create a separate row in genes.txt
    while read -r final_gene_name; do
        echo -e "$final_gene_name\t$base_name\thttps://github.com/mdmparis/defense-finder-models" >> "$destination_folder/genes.txt"
    done <<< "$gene_counts"

    # Modify the NAME field in the .hmm file
    awk '/^NAME/ {if (++count[$2] == 1) print $1, $2; else print $1, $2"_"count[$2]} !/^NAME/ {print $0}' "$file" > "$file.tmp" && mv "$file.tmp" "$file"
done

# Concatenate .hmm files into genes.hmm
cat "$source_folder/profiles"/*.hmm > "$destination_folder/genes.hmm"

# Compress genes.hmm using gzip
gzip "$destination_folder/genes.hmm"

# Delete
rm -r $source_folder

# Display completion message
echo "Script completed successfully. Files are in $destination_folder."