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)