Importing autoDCR to other scripts

If an application were to require V/J/CDR3 (and potentially even constant and/or leader sequence) annotation, there are various ways to import autoDCR functionality into other Python scripts. Perhaps the simplest way is to import the function which underlies autoDCR cli, as this provides a versatile interface to perform different kinds of TCR annotation. Assuming reference data has been suitably processed, users can do the following:

# Import the necessary bits and bobs
from autoDCRscripts import commandline as cli
from autoDCRscripts.main import data_dir

# Let's pick a couple of TCR sequences
in_tcr_nt = ('GGGTTTTTCTGCTGTGGGTACGTGAGCAGGAAACATGGAGAAGAATCCTTTGGCAGCCCCATTACTAATCCTCTGGTTTCATCTTGACTGCGTGAGCAGCATACT'
             'GAACGTGGAACAAAGTCCTCAGTCACTGCATGTTCAGGAGGGAGACAGCACCAATTTCACCTGCAGCTTCCCTTCCAGCAATTTTTATGCCTTACACTGGTCCAG'
             'ATGGGAAACTGCAAAAAGCCCCGAGGCCTTGTTTGTAATGACTTTAAATGGGGATGAAAAGAAGAAAGGACGAATAAGTGCCACTCTTAATACCAAGGAGGGTTA'
             'CAGCTATTTGTACATCAAAGGATCCCAGCCTGAAGACTCAGCCACATACCTCTGTGCCTTTACTTATGGAGGAAGCCAAGGAAATCTCATCTTTGGAAAAGGCAC'
             'TAAACTCTCTGTTAAACCAAATATCCAGAACCCTGACCCTGACGTG')
in_tcr_aa = ('DSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNIL'
             'ERFSAQQFPDLHSELNLSSLELGDSALYFCASSARSGELFFGEGSRLTVLEDLKNVFPPL')

# Then run the annotation command on them
out_tcr_nt = cli.cli_annotate(tcr=in_tcr_nt, dcr_mode='full', output_mode='return', tcr_name='some-cool-nt-tcr',
                              species='HUMAN', loci='AB', orientation='forward', barcoding=False, protein=False,
                              genbank_mode='read', deletion_limit=30, cdr3_limit=30, data_dir=data_dir)

out_tcr_aa = cli.cli_annotate(in_tcr_aa, 'vjcdr3', 'return', 'tcr', 'HUMAN', 'AB', 'forward',
                              False, True, 'read', 30, 30, data_dir)


# The different components of the detected rearrangements
out_tcr_nt['v_call']
'TRAV24*01'
out_tcr_nt['j_call']
'TRAJ42*01'
out_tcr_nt['l_call']
'TRAV24*01'
out_tcr_nt['junction_aa']
'CAFTYGGSQGNLIF'

out_tcr_aa['v_call']
'TRBV9*01,TRBV9*03'
out_tcr_aa['j_call']
'TRBJ2-2*01'
out_tcr_aa['junction_aa']
'CASSARSGELFF'

Things to note

• The above approach makes use of an additional dcr_mode, ‘return’. This is somewhat analogous to the ‘json’ mode, but instead of saving the output dictionary to a file, it returns it.