PATHOS/setup_pathos.sh at main · DSIMB/PATHOS · GitHub

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#!/bin/bash
# PATHOS Setup Script
# Downloads database files from Zenodo and sets up conda environment
#
# Usage:
#   ./setup_pathos.sh        Download only pathos.db (minimal, required for all predictions)
#   ./setup_pathos.sh all    Download all files including the allele frequency database,
#                            MSA alignments, and mmseqs2 mammalian database (required for
#                            de novo prediction of proteins not in the precomputed database)

set -e

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
DATABASE_DIR="${SCRIPT_DIR}/database"

DOWNLOAD_ALL=false
if [ "${1}" = "all" ]; then
    DOWNLOAD_ALL=true
fi

echo "=== PATHOS Setup ==="

if [ "$DOWNLOAD_ALL" = true ]; then
    echo "Mode: full (pathos.db + af_index.sqlite + MSAs + mmseqs2 database)"
else
    echo "Mode: minimal (pathos.db only)"
    echo "Run './setup_pathos.sh all' to also download files needed for de novo prediction."
fi

# 1. Create conda environment
echo "Creating conda environment..."
conda env create -f env/PATHOS_env.yml


# Function to download and verify file integrity
# Skips download if the file already exists in DATABASE_DIR with a correct MD5
download_and_verify() {
    local url=$1
    local filename=$2
    local expected_md5=$3
    local dest="$DATABASE_DIR/$filename"

    echo "Processing $filename..."

    # Check if already installed in DATABASE_DIR
    if [ -f "$dest" ]; then
        actual_md5=$(md5sum "$dest" | cut -d ' ' -f 1)
        if [ "$actual_md5" = "$expected_md5" ]; then
            echo "$filename already present and verified. Skipping download."
            return 0
        else
            echo "Integrity check failed for existing $dest. Re-downloading..."
        fi
    fi

    # Check if partially downloaded in current directory
    if [ -f "$filename" ]; then
        actual_md5=$(md5sum "$filename" | cut -d ' ' -f 1)
        if [ "$actual_md5" = "$expected_md5" ]; then
            echo "$filename already downloaded. Skipping."
            return 0
        else
            echo "Resuming download of $filename..."
        fi
    fi

    wget -c "$url" -O "$filename"

    actual_md5=$(md5sum "$filename" | cut -d ' ' -f 1)
    if [ "$actual_md5" = "$expected_md5" ]; then
        echo "Integrity verified for $filename."
    else
        echo "ERROR: Integrity check failed for $filename. Expected $expected_md5, got $actual_md5"
        exit 1
    fi
}

# 2. Download database files
echo "Downloading database files from Zenodo..."

# pathos.db — always downloaded
download_and_verify "https://zenodo.org/records/20189718/files/pathos.db?download=1" "pathos.db" "886dc2ace433fee959fc575cc4841652"

if [ "$DOWNLOAD_ALL" = true ]; then
    # mmseqs_db.zip (2.3 GB)
    download_and_verify "https://zenodo.org/records/20189718/files/mmseqs_db.zip?download=1" "mmseqs_db.zip" "c6fea1cc063445a951468328b905031a"

    # MSAs.zip (1.0 GB)
    download_and_verify "https://zenodo.org/records/20189718/files/MSAs.zip?download=1" "MSAs.zip" "5cbfcc3efd622afe92fcdda49104e8d8"

    # af_index.sqlite (1.4 GB)
    download_and_verify "https://zenodo.org/records/20189718/files/af_index.sqlite?download=1" "af_index.sqlite" "63a8e133b56ce22699076562975cff34"
fi

# 3. Extract zip archives and move files
echo "Extracting archives into $DATABASE_DIR..."

if [ -f pathos.db ]; then
    mv pathos.db "$DATABASE_DIR/pathos.db"
fi

if [ "$DOWNLOAD_ALL" = true ]; then
    if [ -f MSAs.zip ]; then
        unzip -o MSAs.zip -d "$DATABASE_DIR" && rm MSAs.zip
    fi
    if [ -f mmseqs_db.zip ]; then
        unzip -o mmseqs_db.zip -d "$DATABASE_DIR" && rm mmseqs_db.zip
    fi
    if [ -f af_index.sqlite ]; then
        mv af_index.sqlite "$DATABASE_DIR/af_index.sqlite"
    fi
fi

if [ -f database/fastas.zip ]; then
    unzip -o database/fastas.zip -d "$DATABASE_DIR" && rm database/fastas.zip
fi
if [ -f database/uniprot.zip ]; then
    unzip -o database/uniprot.zip -d "$DATABASE_DIR" && rm database/uniprot.zip
fi

cd ..

echo ""
echo "=== Setup complete ==="
echo "Activate the environment with: conda activate PATHOS_env"
echo "Test with: python run_pathos.py --protein P51787 --mutation M1A"