def set_final_cyst_tryp_positions(self,
debug=False,
total_length_from_right=-1):
""" Set tryp position in the final, combined sequence. """
self.final_cyst_position = self.local_cyst_position - self.effective_erosions[
'v_5p']
self.final_tryp_position = utils.find_tryp_in_joined_seq(
self.local_tryp_position, self.eroded_seqs['v'],
self.insertions['vd'], self.eroded_seqs['d'],
self.insertions['dj'], self.eroded_seqs['j'],
self.erosions['j_5p'])
if debug:
print ' final tryptophan position: %d' % self.final_tryp_position
# make sure cdr3 length matches the desired length in vdj_combo_label
final_cdr3_length = self.final_tryp_position - self.final_cyst_position + 3
if debug:
print ' final_tryp_position - final_cyst_position + 3 = %d - %d + 3 = %d (should be %d)' % (
self.final_tryp_position, self.final_cyst_position,
final_cdr3_length, self.cdr3_length)
utils.check_both_conserved_codons(
self.eroded_seqs['v'] + self.insertions['vd'] +
self.eroded_seqs['d'] + self.insertions['dj'] +
self.eroded_seqs['j'], self.final_cyst_position,
self.final_tryp_position)
assert final_cdr3_length == int(self.cdr3_length)
assert total_length_from_right == -1 # deprecated (I think) now that I'm adding the mimic_data_read_length option
def set_final_cyst_tryp_positions(self, debug=False):
""" Set tryp position in the final, combined sequence. """
self.final_cyst_position = self.local_cyst_position - self.effective_erosions['v_5p']
self.final_tryp_position = utils.find_tryp_in_joined_seq(self.local_tryp_position,
self.eroded_seqs['v'],
self.insertions['vd'],
self.eroded_seqs['d'],
self.insertions['dj'],
self.eroded_seqs['j'],
self.erosions['j_5p'])
if debug:
print ' final tryptophan position: %d' % self.final_tryp_position
# make sure cdr3 length matches the desired length in vdj_combo_label
final_cdr3_length = self.final_tryp_position - self.final_cyst_position + 3
if debug:
print ' final_tryp_position - final_cyst_position + 3 = %d - %d + 3 = %d (should be %d)' % (self.final_tryp_position, self.final_cyst_position, final_cdr3_length, self.cdr3_length)
utils.check_both_conserved_codons(self.eroded_seqs['v'] + self.insertions['vd'] + self.eroded_seqs['d'] + self.insertions['dj'] + self.eroded_seqs['j'], self.final_cyst_position, self.final_tryp_position)
assert final_cdr3_length == int(self.cdr3_length)
def set_final_cyst_tryp_positions(self, debug=False, total_length_from_right=-1):
""" Set tryp position in the final, combined sequence. """
self.final_cyst_position = self.local_cyst_position - self.effective_erosions["v_5p"]
self.final_tryp_position = utils.find_tryp_in_joined_seq(
self.local_tryp_position,
self.eroded_seqs["v"],
self.insertions["vd"],
self.eroded_seqs["d"],
self.insertions["dj"],
self.eroded_seqs["j"],
self.erosions["j_5p"],
)
if debug:
print " final tryptophan position: %d" % self.final_tryp_position
# make sure cdr3 length matches the desired length in vdj_combo_label
final_cdr3_length = self.final_tryp_position - self.final_cyst_position + 3
if debug:
print " final_tryp_position - final_cyst_position + 3 = %d - %d + 3 = %d (should be %d)" % (
self.final_tryp_position,
self.final_cyst_position,
final_cdr3_length,
self.cdr3_length,
)
utils.check_both_conserved_codons(
self.eroded_seqs["v"]
+ self.insertions["vd"]
+ self.eroded_seqs["d"]
+ self.insertions["dj"]
+ self.eroded_seqs["j"],
self.final_cyst_position,
self.final_tryp_position,
)
assert final_cdr3_length == int(self.cdr3_length)
assert (
total_length_from_right == -1
) # deprecated (I think) now that I'm adding the mimic_data_read_length option
