sc-samap 2.0.0

The SAMap algorithm

SAMap -- version 2.0.0

Citation

Please cite the following paper if using SAMap: https://elifesciences.org/articles/66747

Tarashansky, Alexander J., et al. "Mapping single-cell atlases throughout Metazoa unravels cell type evolution." Elife 10 (2021): e66747.

Installation

pip

pip install sc-samap

Manual installation

Download Anacodna from here: https://www.anaconda.com/download/

Create and activate a new environment for SAMap as follows:

# Install SAMap dependencies availabe in conda
conda create -n SAMap -c conda-forge python=3.9 numpy=1.23.5 pip pybind11 h5py=3.8.0 leidenalg python-igraph texttable
conda activate SAMap

Having activated the environment, install SAMap like so:

git clone https://github.com/atarashansky/SAMap.git samap_directory
cd samap_directory
pip install .

NCBI BLAST must be installed for the commandline.

# Define NCBI BLAST version.
ncbi_blast_version='2.9.0'

# Download NCBI BLAST tarball.
wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbi_blast_version}/ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz"

# Extract NCBI BLAST binaries in current conda environment bin directory.
tar -xzvf "ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz" \
    -C "${CONDA_PREFIX}/bin/" \
    --strip-components=2 \
    "ncbi-blast-${ncbi_blast_version}+/bin/"

Alternatively, add the NCBI BLAST binaries manually to the path:

# Define NCBI BLAST version.
ncbi_blast_version='2.9.0'

# Download NCBI BLAST tarball.
wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbi_blast_version}/ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz"

# Extract NCBI BLAST tarball.
tar -xzvf "ncbi-blast-${ncbi_blast_version}+-x64-linux.tar.gz"

# Add NCBI BLAST programs to PATH.
echo "export PATH=\"$PATH:/your/directory/ncbi-blast-${ncbi_blast_version}+/bin\"" >> ~/.bashrc
source ~/.bashrc

Installation time should take no more than 10 minutes.

Running BLAST

The BLAST mapping script can be run from the SAMap_vignette.ipynb Jupyter notebook.

Depending on the number of cores available on your machine and the size/type of the input fasta files, this step may take up to around 4 hours.

Running SAMap

To run SAMap, use the SAMAP function in samap/mapping.py. Please see its function documentation for a description of the inputs and outputs. Take a look at the provided Jupyter notebook to get started (SAMap_vignette.ipynb).