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Single TCR example

Here's an example of how you can process a single nucleotide sequence:

betaNT = 'CGGGGGGGGTACCNTTGNTTAGGTCCTCTACACGGTTAACCTGGTCCCCGAACCGAAGGTCAATAGGGCCTGTATACTGCTGGCACAGAAGTACACAGCTGAGTCCCTGGGTTCTGAGGGCTGGATCTTCAGAGTGGAGTCANN'

betaQuals = '12.12.12.12.12.22.9.8.6.6.6.8.3.0.3.10.3.0.3.10.10.11.20.25.30.37.37.29.27.14.14.15.27.30.41.47.36.50.50.50.42.42.57.57.43.47.53.47.47.47.47.47.47.50.54.57.57.57.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.57.57.57.57.59.59.59.57.57.57.57.57.57.57.57.59.57.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.68.59.59.59.59.59.57.57.57.59.57.57.43.37.28.28.21.28.23.37.28.30.15.19.17.15.21.20.25.3.0.0'

import tcrdist as td
chain = td.processing.processNT('human', 'B', betaNT, betaQuals)

Pipeline example

Here's an example of a TCR pipeline with tcrdist:

import tcrdist as td
psDf = td.datasets.loadPSData('human_pairseqs_v1')
probDf = td.processing.computeProbs(psDf)
psDf = psDf.join(probDf)
clonesDf = td.processing.identifyClones(psDf)

Testing

To run all tests:

py.test tcrdist

or to pass all print statements through for debugging:

py.test tcrdist -s

Note that importing and running functions in tcrdist generates a log file, tcrdist.log. You can set the logging level by modifying the parameter in the base __init__.py file using one of the following:

logging.ERROR
logging.WARNING
logging.INFO
logging.DEBUG

For details see documentation on the logging module.