def try_to_combine(self, irandom):
"""
Create a recombination event and write it to disk
<irandom> is used as the seed for the myriad random number calls.
If combine() is called with the same <irandom>, it will find the same event, i.e. it should be a random number, not just a seed
"""
if self.args.debug:
print 'combine (seed %d)' % irandom
numpy.random.seed(irandom)
random.seed(irandom)
reco_event = RecombinationEvent(self.glfo)
self.choose_vdj_combo(reco_event)
self.erode_and_insert(reco_event)
if self.args.debug:
print ' joining eroded seqs'
print ' v: %s' % reco_event.eroded_seqs['v']
print ' insert: %s' % reco_event.insertions['vd']
print ' d: %s' % reco_event.eroded_seqs['d']
print ' insert: %s' % reco_event.insertions['dj']
print ' j: %s' % reco_event.eroded_seqs['j']
reco_event.recombined_seq = reco_event.eroded_seqs[
'v'] + reco_event.insertions['vd'] + reco_event.eroded_seqs[
'd'] + reco_event.insertions['dj'] + reco_event.eroded_seqs['j']
reco_event.set_post_erosion_codon_positions()
# set the original conserved codon words, so we can revert them if they get mutated NOTE we do it here, *after* setting the full recombined sequence, so the germline Vs that don't extend through the cysteine don't screw us over
reco_event.unmutated_codons = {}
for region, codon in utils.conserved_codons[self.args.locus].items():
fpos = reco_event.post_erosion_codon_positions[region]
original_codon = reco_event.recombined_seq[fpos:fpos + 3]
reco_event.unmutated_codons[region] = reco_event.recombined_seq[
fpos:fpos + 3]
# print fpos, original_codon, utils.codon_unmutated(codon, reco_event.recombined_seq, fpos)
codons_ok = utils.both_codons_unmutated(
self.glfo['locus'],
reco_event.recombined_seq,
reco_event.post_erosion_codon_positions,
extra_str=' ',
debug=self.args.debug)
if not codons_ok:
if self.args.rearrange_from_scratch and self.args.generate_germline_set: # if you let it try more than once, it screws up the desired allele prevalence ratios
raise Exception('arg')
return False
in_frame = utils.in_frame(
reco_event.recombined_seq, reco_event.post_erosion_codon_positions,
'', reco_event.effective_erosions['v_5p']
) # NOTE empty string is the fv insertion, which is hard coded to zero in event.py. I no longer recall the details of that decision, but I have a large amount of confidence that it's more sensible than it looks
if self.args.rearrange_from_scratch and not in_frame:
raise Exception(
'arg 2'
) # if you let it try more than once, it screws up the desired allele prevalence ratios
return False
self.add_mutants(reco_event, irandom)
reco_event.write_event(self.outfname, reco_event.line)
return True
def try_to_combine(self, irandom):
"""
Create a recombination event and write it to disk
<irandom> is used as the seed for the myriad random number calls.
If combine() is called with the same <irandom>, it will find the same event, i.e. it should be a random number, not just a seed
"""
if self.args.debug:
print 'combine (seed %d)' % irandom
numpy.random.seed(irandom)
random.seed(irandom)
reco_event = RecombinationEvent(self.glfo)
self.choose_vdj_combo(reco_event)
self.erode_and_insert(reco_event)
if self.args.debug:
print ' joining eroded seqs'
print ' v: %s' % reco_event.eroded_seqs['v']
print ' insert: %s' % reco_event.insertions['vd']
print ' d: %s' % reco_event.eroded_seqs['d']
print ' insert: %s' % reco_event.insertions['dj']
print ' j: %s' % reco_event.eroded_seqs['j']
reco_event.recombined_seq = reco_event.eroded_seqs['v'] + reco_event.insertions['vd'] + reco_event.eroded_seqs['d'] + reco_event.insertions['dj'] + reco_event.eroded_seqs['j']
codons_ok = reco_event.set_final_cyst_tryp_positions(debug=self.args.debug)
if not codons_ok:
return False
self.add_mutants(reco_event, irandom) # toss a bunch of clones: add point mutations
if self.args.debug:
reco_event.print_event()
# write output to csv
reco_event.write_event(self.outfname, irandom=irandom)
return True
def try_to_combine(self, irandom):
"""
Create a recombination event and write it to disk
<irandom> is used as the seed for the myriad random number calls.
If combine() is called with the same <irandom>, it will find the same event, i.e. it should be a random number, not just a seed
"""
if self.args.debug:
print 'combine (seed %d)' % irandom
numpy.random.seed(irandom)
random.seed(irandom)
reco_event = RecombinationEvent(self.glfo)
self.choose_vdj_combo(reco_event)
self.erode_and_insert(reco_event)
if self.args.debug:
print ' joining eroded seqs'
print ' v: %s' % reco_event.eroded_seqs['v']
print ' insert: %s' % reco_event.insertions['vd']
print ' d: %s' % reco_event.eroded_seqs['d']
print ' insert: %s' % reco_event.insertions['dj']
print ' j: %s' % reco_event.eroded_seqs['j']
reco_event.recombined_seq = reco_event.eroded_seqs['v'] + reco_event.insertions['vd'] + reco_event.eroded_seqs['d'] + reco_event.insertions['dj'] + reco_event.eroded_seqs['j']
reco_event.set_final_codon_positions()
# set the original conserved codon words, so we can revert them if they get mutated NOTE we do it here, *after* setting the full recombined sequence, so the germline Vs that don't extend through the cysteine don't screw us over
reco_event.unmutated_codons = {}
for region, codon in utils.conserved_codons[self.args.chain].items():
fpos = reco_event.final_codon_positions[region]
original_codon = reco_event.recombined_seq[fpos : fpos + 3]
reco_event.unmutated_codons[region] = reco_event.recombined_seq[fpos : fpos + 3]
# print fpos, original_codon, utils.codon_ok(codon, reco_event.recombined_seq, fpos)
codons_ok = utils.both_codons_ok(self.glfo['chain'], reco_event.recombined_seq, reco_event.final_codon_positions, extra_str=' ', debug=self.args.debug)
if not codons_ok:
if self.args.rearrange_from_scratch and self.args.generate_germline_set: # if you let it try more than once, it screws up the desired allele prevalence ratios
raise Exception('arg')
return False
in_frame = reco_event.cdr3_length % 3 == 0
if self.args.rearrange_from_scratch and not in_frame:
raise Exception('arg 2') # if you let it try more than once, it screws up the desired allele prevalence ratios
return False
self.add_mutants(reco_event, irandom) # toss a bunch of clones: add point mutations
if self.args.debug:
reco_event.print_event()
# write output to csv
reco_event.write_event(self.outfname, irandom=irandom)
return True
def combine(self, irandom):
"""
Create a recombination event and write it to disk
<irandom> is used as the seed for the myriad random number calls.
If combine() is called with the same <irandom>, it will find the same event, i.e. it should be a random number, not just a seed
"""
if self.args.debug:
print 'combine (seed %d)' % irandom
numpy.random.seed(irandom)
random.seed(irandom)
reco_event = RecombinationEvent(self.all_seqs)
self.choose_vdj_combo(reco_event)
self.erode_and_insert(reco_event)
if self.args.debug:
print ' joining eroded seqs'
print ' v: %s' % reco_event.eroded_seqs['v']
print ' insert: %s' % reco_event.insertions['vd']
print ' d: %s' % reco_event.eroded_seqs['d']
print ' insert: %s' % reco_event.insertions['dj']
print ' j: %s' % reco_event.eroded_seqs['j']
reco_event.recombined_seq = reco_event.eroded_seqs[
'v'] + reco_event.insertions['vd'] + reco_event.eroded_seqs[
'd'] + reco_event.insertions['dj'] + reco_event.eroded_seqs['j']
try:
reco_event.set_final_cyst_tryp_positions(
total_length_from_right=self.total_length_from_right,
debug=self.args.debug)
except AssertionError:
print 'ERROR bad conserved codos, what the hell?'
return False
if self.args.naivety == 'M':
self.add_mutants(
reco_event,
irandom) # toss a bunch of clones: add point mutations
else:
reco_event.final_seqs.append(reco_event.recombined_seq)
if self.args.debug:
reco_event.print_event(self.total_length_from_right)
# write output to csv
reco_event.write_event(self.outfname,
self.total_length_from_right,
irandom=irandom)
return True
def combine(self, irandom):
"""
Create a recombination event and write it to disk
<irandom> is used as the seed for the myriad random number calls.
If combine() is called with the same <irandom>, it will find the same event, i.e. it should be a random number, not just a seed
"""
if self.args.debug:
print 'combine (seed %d)' % irandom
numpy.random.seed(irandom)
random.seed(irandom)
reco_event = RecombinationEvent(self.all_seqs)
self.choose_vdj_combo(reco_event)
self.erode_and_insert(reco_event)
if self.args.debug:
print ' joining eroded seqs'
print ' v: %s' % reco_event.eroded_seqs['v']
print ' insert: %s' % reco_event.insertions['vd']
print ' d: %s' % reco_event.eroded_seqs['d']
print ' insert: %s' % reco_event.insertions['dj']
print ' j: %s' % reco_event.eroded_seqs['j']
reco_event.recombined_seq = reco_event.eroded_seqs['v'] + reco_event.insertions['vd'] + reco_event.eroded_seqs['d'] + reco_event.insertions['dj'] + reco_event.eroded_seqs['j']
try:
reco_event.set_final_cyst_tryp_positions(total_length_from_right=self.total_length_from_right, debug=self.args.debug)
except AssertionError:
print 'ERROR bad conserved codos, what the hell?'
return False
if self.args.naivety == 'M':
self.add_mutants(reco_event, irandom) # toss a bunch of clones: add point mutations
else:
reco_event.final_seqs.append(reco_event.recombined_seq)
if self.args.debug:
reco_event.print_event(self.total_length_from_right)
# write output to csv
reco_event.write_event(self.outfname, self.total_length_from_right, irandom=irandom)
return True
