TCRnumba 0.1.6

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To run the script with default parameters, we type

python graph_numba.py 

You receive an overview over parameters by typing

python graph_numba.py -h

The parameter N sets the number of CDR3 beta sequences, which is loaded. N_part refers to the length of a single block. Moreover, len_xy defines the number of blocks in a single row. N should always be chosen, so that

N >= len_xy * N_part.

The script results in produces a txt file, containing the sparse adjacency matrix, that contains the single-number indices of the edges. Moreover, the script ii

Graph_tool

Necessary for running the file make_net.py is the package "graph_tool". On Linux it can be installed via

conda create --name gt -c conda-forge graph-tool
conda activate gt

For detailed instructions see the homepage https://graph-tool.skewed.de/. Since "graph_tool" is incompatible with numba, "graph_tool" has to be deactivated to run the files "graph_numba.py" or "convert_indices.py". You can do that via

conda deactivate
conda activate

Make sure that at the beginning of each line in the terminal we see "(base)", not "(gt)". To run "make_net.py" you can activate "graph_tool" again using

conda activate gt

Use the command line to execute files.

The scripts can be run from the Command line. Examples are

python graph_numba.py --N=10 --N_part=2 --len_xy=5 --src=test_data.txt
python convert_indices.py --single_sidelength=2 --len_xy=5 --format=dense
python graph_ref.py --N=10 --src="test_data.txt"

Don't write input numbers as exponentials, e.g. write 5000 instead of 5*10**3.

Calculate the adjacency matrix within python by directly inputting the string array:

import graph_numba as gn
import convert_pure as cp

adjacency_sparse = gn.adjacency_matrix(['ABC', 'DEF', 'EFG', 'ABC', 'ABD', 'EEE', 'EEF', 'EFF', 'GGE', 'GAS'], N_part=2, len_xy=5, direct_output=True)
cp.convert_pure(adjacency_sparse, 2, 5)

print(adjacency_sparse)

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Use SONIA to create files

sonia-generate --humanTRB -n 1000000 --pre -o pre_example.txt