def set_vdj_combo(
self, vdj_combo_label, cyst_positions, tryp_positions, all_seqs, debug=False, dont_mimic_data_read_length=False
):
""" Set the label which labels the gene/length choice (a tuple of strings) as well as it's constituent parts """
self.vdj_combo_label = vdj_combo_label
for region in utils.regions:
self.genes[region] = vdj_combo_label[utils.index_keys[region + "_gene"]]
self.original_seqs[region] = all_seqs[region][self.genes[region]]
self.original_seqs[region] = self.original_seqs[region].replace(
"N", utils.int_to_nucleotide(random.randint(0, 3))
) # replace any Ns with a random nuke (a.t.m. use the same nuke for all Ns in a given seq)
self.local_cyst_position = cyst_positions[self.genes["v"]]["cysteine-position"] # cyst position in uneroded v
self.local_tryp_position = int(tryp_positions[self.genes["j"]]) # tryp position within j only
self.cdr3_length = int(vdj_combo_label[utils.index_keys["cdr3_length"]])
for boundary in utils.boundaries:
self.insertion_lengths[boundary] = int(vdj_combo_label[utils.index_keys[boundary + "_insertion"]])
for erosion in utils.real_erosions:
self.erosions[erosion] = int(vdj_combo_label[utils.index_keys[erosion + "_del"]])
for erosion in utils.effective_erosions:
if not dont_mimic_data_read_length: # use v left and j right erosions from data?
self.effective_erosions[erosion] = int(vdj_combo_label[utils.index_keys[erosion + "_del"]])
else: # otherwise ignore data, and keep the entire v and j genes
self.effective_erosions[erosion] = 0
# set the original conserved codon words, so we can revert them if they get mutated
self.original_cyst_word = str(self.original_seqs["v"][self.local_cyst_position : self.local_cyst_position + 3])
self.original_tryp_word = str(self.original_seqs["j"][self.local_tryp_position : self.local_tryp_position + 3])
if debug:
self.print_gene_choice()
def set_vdj_combo(self,
vdj_combo_label,
glfo,
debug=False,
mimic_data_read_length=False):
""" Set the label which labels the gene/length choice (a tuple of strings) as well as it's constituent parts """
self.vdj_combo_label = vdj_combo_label
for region in utils.regions:
self.genes[region] = vdj_combo_label[utils.index_keys[region +
'_gene']]
self.original_seqs[region] = glfo['seqs'][region][
self.genes[region]]
self.original_seqs[region] = self.original_seqs[region].replace(
'N', utils.int_to_nucleotide(random.randint(0, 3))
) # replace any Ns with a random nuke (a.t.m. use the same nuke for all Ns in a given seq)
for region, codon in utils.conserved_codons[glfo['locus']].items():
self.pre_erosion_codon_positions[region] = glfo[
codon + '-positions'][
self.genes[region]] # position in uneroded germline gene
for boundary in utils.boundaries:
self.insertion_lengths[boundary] = int(
vdj_combo_label[utils.index_keys[boundary + '_insertion']])
for erosion in utils.real_erosions:
self.erosions[erosion] = int(
vdj_combo_label[utils.index_keys[erosion + '_del']])
for erosion in utils.effective_erosions:
if mimic_data_read_length: # use v left and j right erosions from data?
self.effective_erosions[erosion] = int(
vdj_combo_label[utils.index_keys[erosion + '_del']])
else: # otherwise ignore data, and keep the entire v and j genes
self.effective_erosions[erosion] = 0
if debug:
self.print_gene_choice()
def set_vdj_combo(self,
vdj_combo_label,
cyst_positions,
tryp_positions,
all_seqs,
debug=False,
dont_mimic_data_read_length=False):
""" Set the label which labels the gene/length choice (a tuple of strings) as well as it's constituent parts """
self.vdj_combo_label = vdj_combo_label
for region in utils.regions:
self.genes[region] = vdj_combo_label[utils.index_keys[region +
'_gene']]
self.original_seqs[region] = all_seqs[region][self.genes[region]]
self.original_seqs[region] = self.original_seqs[region].replace(
'N', utils.int_to_nucleotide(random.randint(0, 3))
) # replace any Ns with a random nuke (a.t.m. use the same nuke for all Ns in a given seq)
self.local_cyst_position = cyst_positions[self.genes['v']][
'cysteine-position'] # cyst position in uneroded v
self.local_tryp_position = int(
tryp_positions[self.genes['j']]) # tryp position within j only
self.cdr3_length = int(
vdj_combo_label[utils.index_keys['cdr3_length']])
for boundary in utils.boundaries:
self.insertion_lengths[boundary] = int(
vdj_combo_label[utils.index_keys[boundary + '_insertion']])
for erosion in utils.real_erosions:
self.erosions[erosion] = int(
vdj_combo_label[utils.index_keys[erosion + '_del']])
for erosion in utils.effective_erosions:
if not dont_mimic_data_read_length: # use v left and j right erosions from data?
self.effective_erosions[erosion] = int(
vdj_combo_label[utils.index_keys[erosion + '_del']])
else: # otherwise ignore data, and keep the entire v and j genes
self.effective_erosions[erosion] = 0
# set the original conserved codon words, so we can revert them if they get mutated
self.original_cyst_word = str(
self.original_seqs['v']
[self.local_cyst_position:self.local_cyst_position + 3])
self.original_tryp_word = str(
self.original_seqs['j']
[self.local_tryp_position:self.local_tryp_position + 3])
if debug:
self.print_gene_choice()
def set_vdj_combo(self, vdj_combo_label, glfo, debug=False, mimic_data_read_length=False):
""" Set the label which labels the gene/length choice (a tuple of strings) as well as it's constituent parts """
self.vdj_combo_label = vdj_combo_label
for region in utils.regions:
self.genes[region] = vdj_combo_label[utils.index_keys[region + '_gene']]
self.original_seqs[region] = glfo['seqs'][region][self.genes[region]]
self.original_seqs[region] = self.original_seqs[region].replace('N', utils.int_to_nucleotide(random.randint(0, 3))) # replace any Ns with a random nuke (a.t.m. use the same nuke for all Ns in a given seq)
for region, codon in utils.conserved_codons[glfo['chain']].items():
self.local_codon_positions[region] = glfo[codon + '-positions'][self.genes[region]] # position in uneroded germline gene
for boundary in utils.boundaries:
self.insertion_lengths[boundary] = int(vdj_combo_label[utils.index_keys[boundary + '_insertion']])
for erosion in utils.real_erosions:
self.erosions[erosion] = int(vdj_combo_label[utils.index_keys[erosion + '_del']])
for erosion in utils.effective_erosions:
if mimic_data_read_length: # use v left and j right erosions from data?
self.effective_erosions[erosion] = int(vdj_combo_label[utils.index_keys[erosion + '_del']])
else: # otherwise ignore data, and keep the entire v and j genes
self.effective_erosions[erosion] = 0
if debug:
self.print_gene_choice()
