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.
pip install samap
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=3.7 pip pybind11 h5py=2.10.0 leidenalg python-igraph texttable
conda activate SAMapHaving 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 ~/.bashrcInstallation time should take no more than 10 minutes.
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.
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).
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