timsbuktoolkit/run.bash at main · TalusBio/timsbuktoolkit · GitHub

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set -x
set -e

if [ -n "${FULL_RUN}" ]; then
    # Full run
    echo "Full run"
    sleep 2
    FASTA_FILE="$HOME/fasta/20231030_LINEARIZED_UP000005640_9606.fasta"
    SPECLIB_NAME="data_ignore/20231030_LINEARIZED_UP000005640_9606.msgpack.zstd"
    DOTD_FILE="/Users/sebastianpaez/git/ionmesh/benchmark/240402_PRTC_01_S1-A1_1_11342.d"
    RESULTS_DIR="data_ignore/hela_search_results"
    SUMMARY_DIR="data_ignore/hela_search_summary"
elif [ -n "${FULL_MCCOSS}" ]; then
    echo "Bo data run"
    sleep 2
    DOTD_FILE="$HOME/data/bo_maccoss/N20211212chenc_WOSP00101_DIA_60min_K562_rep1_1_Slot2-37_1_9898.d"
    FASTA_FILE="$HOME/fasta/20231030_LINEARIZED_UP000005640_9606.fasta"
    SPECLIB_NAME="data_ignore/20231030_LINEARIZED_UP000005640_9606.msgpack.zstd"
    RESULTS_DIR="data_ignore/mccoss_search_results"
    SUMMARY_DIR="data_ignore/mccoss_search_summary"
elif [ -n "${VIMENTIN_ONLY}" ]; then
    echo "VIM only"
    sleep 2
    DOTD_FILE="$HOME/git/ionmesh/benchmark/240402_PRTC_01_S1-A1_1_11342.d"
    FASTA_FILE="$HOME/fasta/VIMENTIN.fasta"
    SPECLIB_NAME="data_ignore/vimentin.msgpack.zstd"
    RESULTS_DIR="data_ignore/vimentin_search_results"
    SUMMARY_DIR="data_ignore/vimentin_search_summary"
else
    # Quick run
    echo "Quick run"
    sleep 2
    FASTA_FILE="$HOME/fasta/hela_gt20peps.fasta"
    SPECLIB_NAME="data_ignore/asdad.msgpack.zstd"
    DOTD_FILE="$HOME/git.bkp/ionmesh/benchmark/240402_PRTC_01_S1-A1_1_11342.d"
    RESULTS_DIR="data_ignore/top_proteins_hela"
    SUMMARY_DIR="data_ignore/top_proteins_hela_summary"
fi

# Stop if the results dir already exists
if [ -d "$RESULTS_DIR" ]; then
    echo "Results dir already exists ${RESULTS_DIR}"
    exit 1
fi


cat << EOF > config_use.json
{
    "analysis": {
        "chunk_size": 20000,
        "tolerance": {
            "ms": {"ppm":  [15.0, 15.0]},
            "mobility": {"percent": [5.0, 5.0]},
            "quad": {"absolute": [0.1, 0.1]}
        }
    }
}
EOF

if [ -f "$SPECLIB_NAME" ]; then
    sleep 2
    echo "Speclib already built"
else
    echo "Building speclib"
    sleep 2
    uv run speclib_build_fasta \
        --fasta_file $FASTA_FILE \
        --decoy_strategy REVERSE \
        --max_ions 10 \
        --outfile $SPECLIB_NAME \
        --model onnx
fi

cargo run --release --bin timsseek -- \
    --config config_use.json \
    --speclib-file $SPECLIB_NAME \
    --output-dir $RESULTS_DIR \
    --dotd-file $DOTD_FILE

# Technically does T/D competition
uv run python -m timsseek_rescore --results_dir $RESULTS_DIR --output_dir $SUMMARY_DIR