schrodinger.application.bioluminate.update_germline_db.translate_db module

Translate OGRDB germline database DNA sequences to amino acid sequences.

Uses database sequences from https://ogrdb.airr-community.org/

class schrodinger.application.bioluminate.update_germline_db.translate_db.Locus(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

HEAVY = 'IGH'

KAPPA = 'IGK'

LAMBDA = 'IGL'

LIGHT = 'IGKL'

ALPHA = 'TRA'

BETA = 'TRB'

GAMMA = 'TRG'

DELTA = 'TRD'

class schrodinger.application.bioluminate.update_germline_db.translate_db.Gene(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: enum.Enum

V = 'V'

D = 'D'

J = 'J'

C = 'C'

class schrodinger.application.bioluminate.update_germline_db.translate_db.GermlineEntry(dna_record: Bio.SeqRecord.SeqRecord)

Bases: object

__init__(dna_record: Bio.SeqRecord.SeqRecord)

property translated_record

static parse_name(name)

schrodinger.application.bioluminate.update_germline_db.translate_db.main()

schrodinger.application.bioluminate.update_germline_db.translate_db.parse_args(argv=None)

schrodinger.application.bioluminate.update_germline_db.translate_db.generate_records(filename)

schrodinger.application.bioluminate.update_germline_db.translate_db.categorize_entries_by_locus(germline_entries, combine_light_chains=True)

schrodinger.application.bioluminate.update_germline_db.translate_db.write_translated_gene_fastas(gene_entries_by_locus, jobname)