Kmerseek

Compiling on Mac

You may need to add these magical export commands to make your Python install work:

export MACOSX_DEPLOYMENT_TARGET=10.15 \
	&& export PYTHON_CONFIGURE_OPTS="--enable-framework" \
	&& export PYTHON_SYS_EXECUTABLE="$(which python)" \
	&& export PYO3_PYTHON="$(which python)" \
	&& export PYTHONPATH="/Users/olga/anaconda3/envs/kmerseek-dev/lib/python3.13/site-packages:$PYTHONPATH" \
	&& export DYLD_FALLBACK_LIBRARY_PATH="/Users/olga/anaconda3/envs/kmerseek-dev/lib:$DYLD_FALLBACK_LIBRARY_PATH" \
	&& export RUSTFLAGS="-C link-arg=-undefined -C link-arg=dynamic_lookup"

It may look like this:

export MACOSX_DEPLOYMENT_TARGET=10.15 \
        && export PYTHON_CONFIGURE_OPTS="--enable-framework" \
        && export PYTHON_SYS_EXECUTABLE="/Users/olga/anaconda3/envs/kmerseek-dev/bin/python" \
        && export PYO3_PYTHON="/Users/olga/anaconda3/envs/kmerseek-dev/bin/python" \
        && export PYTHONPATH="/Users/olga/anaconda3/envs/kmerseek-dev/lib/python3.13/site-packages:$PYTHONPATH" \
        && export DYLD_FALLBACK_LIBRARY_PATH="/Users/olga/anaconda3/envs/kmerseek-dev/lib:$DYLD_FALLBACK_LIBRARY_PATH" \
        && export RUSTFLAGS="-C link-arg=-undefined -C link-arg=dynamic_lookup"

Testing

Run real-world examples like:

cargo run --example test_bcl2_processing

Using the Builder Pattern

The ProteomeIndex now supports a fluent Builder pattern:

use kmerseek::index::ProteomeIndex;

// Using the builder pattern
let index = ProteomeIndex::builder()
    .path("/path/to/database.db")
    .ksize(5)
    .scaled(1)
    .moltype("protein")
    .build()?;

// With auto filename generation
let index = ProteomeIndex::builder()
    .path("/path/to/base")
    .ksize(5)
    .scaled(1)
    .moltype("protein")
    .build_with_auto_filename()?;

// With raw sequence storage
let index = ProteomeIndex::builder()
    .path("/path/to/database.db")
    .ksize(5)
    .scaled(1)
    .moltype("protein")
    .store_raw_sequences(true)
    .build()?;

You can also use convenience methods:

// Create a new index
let index = ProteomeIndex::new_simple(
    "/path/to/database.db",
    5,        // k-mer size
    1,        // scaled
    "protein", // molecular type
    false,    // don't store raw sequences
)?;

// With auto filename generation
let index = ProteomeIndex::new_with_auto_filename_simple(
    "/path/to/data.fasta",
    5,        // k-mer size
    1,        // scaled
    "protein", // molecular type
    false,    // don't store raw sequences
)?;

Run the builder pattern demo:

cargo run --example builder_pattern_demo