def evaluate(self, true_line, inf_line, simglfo=None):
if len(inf_line['unique_ids']) > 1:
raise Exception('mutli-seq lines not yet handled')
iseq = 0
def addval(col, simval, infval):
if col[2:] == '_insertion': # stored as the actual inserted bases
simval = len(simval)
infval = len(infval)
diff = infval - simval
if diff not in self.values[col]:
self.values[col][diff] = 0
self.values[col][diff] += 1
if indelutils.has_indels(true_line['indelfos'][iseq]) or indelutils.has_indels(inf_line['indelfos'][iseq]):
simlen = indelutils.net_length(true_line['indelfos'][iseq])
inflen = indelutils.net_length(inf_line['indelfos'][iseq])
addval('shm_indel_length', simlen, inflen)
if simlen != inflen: # this is probably because the simulated shm indel was within the cdr3, so we attempt to fix it by switching the sim line to non-reversed
print ' %s true and inferred shm net indel lengths different, so skipping rest of performance evaluation' % ' '.join(inf_line['unique_ids'])
# note that you can't really evaluate the rest of the performance vars in a particularly meaningful when the indel info is different (like I tried to do below) since you have to decide how to assign the indel'd bases (like, is it correct to assign the indel'd bases to a deletion? or to an insertion? or to the j?)
return
# true_line = copy.deepcopy(true_line)
# utils.remove_all_implicit_info(true_line)
# true_line['indelfos'][iseq] = indelutils.get_empty_indel()
# true_line['seqs'][iseq] = true_line['input_seqs'][iseq]
# utils.add_implicit_info(simglfo, true_line)
mutfo = {lt : {mt : {} for mt in ['freq', 'total']} for lt in ['sim', 'inf']}
for rstr in plotconfig.rstrings:
if rstr == '': # these are already in the <line>s, so may as well not recalculate
mutfo['sim']['freq'][rstr], mutfo['sim']['total'][rstr] = true_line['mut_freqs'][iseq], true_line['n_mutations'][iseq]
mutfo['inf']['freq'][rstr], mutfo['inf']['total'][rstr] = inf_line['mut_freqs'][iseq], inf_line['n_mutations'][iseq]
else:
mutfo['sim']['freq'][rstr], mutfo['sim']['total'][rstr] = utils.get_mutation_rate_and_n_muted(true_line, iseq=iseq, restrict_to_region=rstr.rstrip('_'))
mutfo['inf']['freq'][rstr], mutfo['inf']['total'][rstr] = utils.get_mutation_rate_and_n_muted(inf_line, iseq=iseq, restrict_to_region=rstr.rstrip('_'))
for col in plotconfig.gene_usage_columns:
self.set_bool_column(true_line, inf_line, col, mutfo['sim']['freq']['']) # this also sets the fraction-correct-vs-mute-freq hists
for column in plotconfig.int_columns:
addval(column, true_line[column], inf_line[column])
for rstr in plotconfig.rstrings:
addval(rstr + 'hamming_to_true_naive', 0, self.hamming_to_true_naive(true_line, inf_line, restrict_to_region=rstr.rstrip('_')))
addval(rstr + 'muted_bases', mutfo['sim']['total'][rstr], mutfo['inf']['total'][rstr])
for region in utils.regions:
if region + '_per_gene_support' in inf_line:
self.set_per_gene_support(true_line, inf_line, region)
self.hists['mute_freqs'].fill(mutfo['inf']['freq'][''] - mutfo['sim']['freq']['']) # when we're evaluating on multi-seq hmm output, we synthesize single-sequence lines for each sequence
def check_seed_for_indels(cluster_line, seed_id, partition_file):
iseq_seed = cluster_line["unique_ids"].index(seed_id)
if indelutils.has_indels(cluster_line["indelfos"][iseq_seed]):
print(indelutils.get_dbg_str(cluster_line["indelfos"][iseq_seed]))
raise Exception(
"indel in seed sequence {}. Options are 1. Look at the annotation for this cluster and find the indel in the seed. Rerun process_partis.py with --match-indel-in-uid <uid-of-seq-containing-indel-of-interest> to process only sequences containing that specific indel for further analysis of the indel 2. Run with --ignore-seed-indels. PS check out {}"
.format(seed_id, partition_file))
def setline(self, irandom=None): # don't access <self.line> directly
if self.line is not None:
return self.line
line = {}
for region in utils.regions:
line[region + '_gene'] = self.genes[region]
for boundary in utils.boundaries:
line[boundary + '_insertion'] = self.insertions[boundary]
for boundary in utils.effective_boundaries:
line[boundary + '_insertion'] = '' # NOTE 'fv' and 'jf' insertions are hereby hardcoded to zero (I'm just writing this here to make it easily searchable -- I don't remember why it's set up that way)
for erosion in utils.real_erosions:
line[erosion + '_del'] = self.erosions[erosion]
for erosion in utils.effective_erosions:
line[erosion + '_del'] = self.effective_erosions[erosion]
line['input_seqs'] = self.final_seqs
line['indelfos'] = self.indelfos
line['seqs'] = [self.indelfos[iseq]['reversed_seq'] if indelutils.has_indels(self.indelfos[iseq]) else line['input_seqs'][iseq] for iseq in range(len(line['input_seqs']))]
self.set_ids(line, irandom=irandom)
treeutils.translate_labels(self.tree, zip(self.leaf_names, line['unique_ids'])) # ordering in <self.leaf_names> is set in recombinator.add_mutants()
line['affinities'] = [None for _ in line['unique_ids']]
line['tree'] = self.tree.as_string(schema='newick')
utils.add_implicit_info(self.glfo, line)
self.line = line
def setline(self, irandom=None): # don't access <self.line> directly
if self.line is not None:
return self.line
line = {}
for region in utils.regions:
line[region + '_gene'] = self.genes[region]
for boundary in utils.boundaries:
line[boundary + '_insertion'] = self.insertions[boundary]
for boundary in utils.effective_boundaries:
line[boundary + '_insertion'] = ''
for erosion in utils.real_erosions:
line[erosion + '_del'] = self.erosions[erosion]
for erosion in utils.effective_erosions:
line[erosion + '_del'] = self.effective_erosions[erosion]
line['input_seqs'] = self.final_seqs
line['indelfos'] = self.indelfos
line['seqs'] = [
line['indelfos'][iseq]['reversed_seq'] if indelutils.has_indels(
line['indelfos'][iseq]) else line['input_seqs'][iseq]
for iseq in range(len(line['input_seqs']))
]
self.set_ids(line, irandom)
utils.add_implicit_info(self.glfo, line)
self.line = line
def get_cluster_meta_dict(cluster_line, seed_id, args):
has_indels = any([
indelutils.has_indels(cluster_line["indelfos"][iseq])
for iseq in range(len(cluster_line["input_seqs"]))
])
if not args.indel_reversed_seqs and not has_indels:
warnings.warn(
"{}: --indel-reversed-seqs was not passed and there are no indels. If running this script from CFT, this is probably because CFT was run with --preserve-indels and there are no indels in this cluster. It will get aligned anyway."
.format(utils.color("red", "warning")))
return {
"sequences": get_cluster_seqs_dict(cluster_line, seed_id, args),
"cdr3_start": cluster_line["codon_positions"]["v"],
"has_seed": seed_id in cluster_line["unique_ids"],
"mean_mut_freq": numpy.mean(cluster_line["mut_freqs"]),
"seed_id": seed_id,
"match_indel_in_uid": args.match_indel_in_uid is not None,
"has_indels": has_indels,
"indels_reversed": has_indels and args.indel_reversed_seqs,
}
def print_seq_in_reco_event(original_line,
iseq,
extra_str='',
label='',
one_line=False,
seed_uid=None,
check_line_integrity=False):
"""
Print ascii summary of recombination event and mutation.
If <one_line>, then skip the germline lines, and only print the final_seq line.
"""
line = original_line
if check_line_integrity: # it's very important not to modify <line> -- this lets you verify that you aren't
line = copy.deepcopy(
original_line) # copy that we can modify without changing <line>
delstrs = {
d: '.' * line[d + '_del']
for d in utils.all_erosions
} # NOTE len(delstrs[<del>]) is not in general the same as len(line[<del>_del])
if len(
delstrs['v_5p']
) > 50: # don't print a million dots if left-side v deletion is really big
delstrs['v_5p'] = '.%d.' % len(delstrs['v_5p'])
# if there isn't enough space for dots in the vj line, we add some dashes to everybody so things fit (rare in heavy chain rearrangements, but pretty common in light chain)
d_plus_inserts_length = len(line['vd_insertion'] + line['d_gl_seq'] +
line['dj_insertion'])
if line['v_3p_del'] + line[
'j_5p_del'] > d_plus_inserts_length: # if dots for v and j interior deletions will be longer than <d_plus_inserts_length>
delstrs['v_3p'] = '.%d.' % line['v_3p_del']
delstrs['j_5p'] = '.%d.' % line['j_5p_del']
gapstr = '-' * (len(delstrs['v_3p'] + delstrs['j_5p']) -
d_plus_inserts_length)
gap_insert_point = len(
line['fv_insertion'] + delstrs['v_5p'] + line['v_gl_seq']
) # it doesn't really matter exactly where we put the blue dashes, as long as it's the same place in all four lines, but this is a good spot
extra_space_because_of_fixed_nospace = max(
0, d_plus_inserts_length - len(delstrs['v_3p'] + delstrs['j_5p'])
) # if shortening the <delstrs> already over-compensated for the lack of space (i.e., if the number of dashes necessary is zero), then we need to add some dots to the vj line below
else:
gapstr = ''
gap_insert_point = None
extra_space_because_of_fixed_nospace = 0
eroded_seqs_dots = {
r: delstrs[r + '_5p'] + line[r + '_gl_seq'] + delstrs[r + '_3p']
for r in utils.regions
}
# build the three germline lines
insert_line = ' ' * (len(line['fv_insertion']) + line['lengths']['v'] + len(delstrs['v_5p'])) \
+ line['vd_insertion'] + ' ' * line['lengths']['d'] + line['dj_insertion'] \
+ ' ' * (line['lengths']['j'] + line['j_3p_del'] + len(line['jf_insertion']))
germline_d_start = len(line['fv_insertion']) + line['lengths']['v'] + len(
line['vd_insertion']) - line['d_5p_del']
germline_d_end = germline_d_start + line['d_5p_del'] + line['lengths'][
'd'] + line['d_3p_del']
d_line = ' ' * (germline_d_start + len(delstrs['v_5p'])) \
+ eroded_seqs_dots['d'] \
+ ' ' * (len(line['j_gl_seq']) + len(line['dj_insertion']) - line['d_3p_del'] + line['j_3p_del'] + len(line['jf_insertion']))
germline_v_end = len(line['fv_insertion']) + len(line['v_gl_seq']) + line[
'v_3p_del'] - 1 # position in the query sequence at which we find the last base of the v match. NOTE we subtract off the v_5p_del because we're *not* adding dots for that deletion (it's just too long)
germline_j_start = germline_d_end + 1 - line['d_3p_del'] + len(
line['dj_insertion']) - line['j_5p_del']
vj_line = ' ' * len(line['fv_insertion']) + eroded_seqs_dots['v'] + '.' * extra_space_because_of_fixed_nospace \
+ ' ' * (germline_j_start - germline_v_end - 2) + eroded_seqs_dots['j'] + ' ' * len(line['jf_insertion'])
# and the query line
qrseq_line = ' ' * len(
delstrs['v_5p']) + line['seqs'][iseq] + ' ' * line['j_3p_del']
outstrs = [insert_line, d_line, vj_line, qrseq_line]
check_outsr_lengths(
line, outstrs, fix=True
) # I think the only way they can be different is if the d right side erosion is so long that it hangs over the right side of the j
if gap_insert_point is not None:
for istr in [
0, 1, 3
]: # everybody except the vj line, which already has the modified interior delstrs above
outstrs[
istr] = outstrs[istr][:gap_insert_point] + gapstr + outstrs[
istr][gap_insert_point:]
check_outsr_lengths(line, outstrs, fix=True)
colors = [[[] for _ in range(len(ostr))] for ostr in outstrs]
if indelutils.has_indels(line['indelfos'][iseq]):
# outstrs, colors = old_indel_shenanigans(line, iseq, outstrs, colors)
outstrs, colors = indel_shenanigans(line, iseq, outstrs, colors)
outstrs = add_colors(outstrs, colors, line)
suffixes = [
'insert%s\n' %
('s' if utils.has_d_gene(utils.get_locus(line['v_gene'])) else ''),
'%s\n' % (utils.color_gene(line['d_gene'])),
'%s %s\n' %
(utils.color_gene(line['v_gene']), utils.color_gene(line['j_gene'])),
'%s %4.2f mut %s\n' %
(get_uid_str(line, iseq, seed_uid), line['mut_freqs'][iseq],
utils.color('red', utils.is_functional_dbg_str(line, iseq)))
]
outstrs = [
'%s%s %s' % (extra_str, ostr, suf)
for ostr, suf in zip(outstrs, suffixes)
]
if label != '': # this doesn't really work if the edge of the removed string is the middle of a color code... but oh well, it doesn't really happen any more since I shortened the kbound label from waterer.py
offset = max(
0,
len(extra_str) -
2) # skootch <label> this many positions leftward into <extra_str>
removed_str = outstrs[0][offset:offset +
utils.len_excluding_colors(label)]
outstrs[0] = outstrs[0][:offset] + label + outstrs[0][
utils.len_excluding_colors(label) +
offset:] # NOTE this *replaces* the bases in <extra_str> with <label>, which is only fine if they're spaces
if removed_str.strip() != '':
print '%s%s (covered by label \'%s\')' % (
' ' * offset, utils.color('red', removed_str), label)
if one_line:
outstrs = outstrs[-1:] # remove all except the query seq line
elif not utils.has_d_gene(utils.get_locus(line['v_gene'])):
outstrs.pop(1) # remove the d germline line
print ''.join(outstrs),
if check_line_integrity:
if set(line.keys()) != set(original_line.keys()):
raise Exception('ack 1')
for k in line:
if line[k] != original_line[k]:
print 'key %s differs:\n %s\n %s ' % (k, line[k],
original_line[k])
raise Exception('')
def parse_bcr_phylo_output(glfo, naive_line, outdir, ievent):
seqfos = utils.read_fastx(bcr_phylo_fasta_fname(
outdir)) # output mutated sequences from bcr-phylo
assert len(
naive_line['unique_ids']
) == 1 # enforces that we ran naive-only, 1-leaf partis simulation above
assert not indelutils.has_indels(
naive_line['indelfos'][0]) # would have to handle this below
if args.debug:
utils.print_reco_event(naive_line)
reco_info = collections.OrderedDict()
for sfo in seqfos:
mline = copy.deepcopy(naive_line)
utils.remove_all_implicit_info(mline)
del mline['tree']
mline['unique_ids'] = [sfo['name']]
mline['seqs'] = [
sfo['seq']
] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['input_seqs'] = [
sfo['seq']
] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['duplicates'] = [[]]
reco_info[sfo['name']] = mline
utils.add_implicit_info(glfo, mline)
final_line = utils.synthesize_multi_seq_line_from_reco_info(
[sfo['name'] for sfo in seqfos], reco_info)
if args.debug:
utils.print_reco_event(final_line)
# extract kd values from pickle file (use a separate script since it requires ete/anaconda to read)
if args.stype == 'selection':
cmd = './bin/read-bcr-phylo-trees.py --pickle-tree-file %s/%s_lineage_tree.p --kdfile %s/kd-vals.csv --newick-tree-file %s/simu.nwk' % (
outdir, args.extrastr, outdir, outdir)
utils.run_ete_script(cmd, ete_path)
nodefo = {}
with open('%s/kd-vals.csv' % outdir) as kdfile:
reader = csv.DictReader(kdfile)
for line in reader:
nodefo[line['uid']] = {
'kd': float(line['kd']),
'relative_kd': float(line['relative_kd']),
'lambda': line.get('lambda', None),
'target_index': int(line['target_index']),
}
if len(
set(nodefo) - set(final_line['unique_ids'])
) > 0: # uids in the kd file but not the <line> (i.e. not in the newick/fasta files) are probably just bcr-phylo discarding internal nodes
print ' in kd file, but missing from final_line (probably just internal nodes that bcr-phylo wrote to the tree without names): %s' % (
set(nodefo) - set(final_line['unique_ids']))
if len(set(final_line['unique_ids']) - set(nodefo)) > 0:
print ' in final_line, but missing from kdvals: %s' % ' '.join(
set(final_line['unique_ids']) - set(nodefo))
final_line['affinities'] = [
1. / nodefo[u]['kd'] for u in final_line['unique_ids']
]
final_line['relative_affinities'] = [
1. / nodefo[u]['relative_kd'] for u in final_line['unique_ids']
]
final_line['lambdas'] = [
nodefo[u]['lambda'] for u in final_line['unique_ids']
]
final_line['nearest_target_indices'] = [
nodefo[u]['target_index'] for u in final_line['unique_ids']
]
tree = treeutils.get_dendro_tree(treefname='%s/simu.nwk' % outdir)
tree.scale_edges(1. / numpy.mean([len(s) for s in final_line['seqs']]))
if args.debug:
print utils.pad_lines(treeutils.get_ascii_tree(dendro_tree=tree),
padwidth=12)
final_line['tree'] = tree.as_string(schema='newick')
tmp_event = RecombinationEvent(
glfo) # I don't want to move the function out of event.py right now
tmp_event.set_reco_id(
final_line, irandom=ievent
) # not sure that setting <irandom> here actually does anything
# get target sequences
target_seqfos = utils.read_fastx('%s/%s_targets.fa' %
(outdir, args.extrastr))
final_line['target_seqs'] = [tfo['seq'] for tfo in target_seqfos]
return final_line
def parse_bcr_phylo_output(glfo, naive_line, outdir, ievent):
seqfos = utils.read_fastx(
'%s/%s.fasta' %
(outdir, args.extrastr)) # output mutated sequences from bcr-phylo
assert len(
naive_line['unique_ids']
) == 1 # enforces that we ran naive-only, 1-leaf partis simulation above
assert not indelutils.has_indels(
naive_line['indelfos'][0]) # would have to handle this below
if args.debug:
utils.print_reco_event(naive_line)
reco_info = collections.OrderedDict()
for sfo in seqfos:
mline = copy.deepcopy(naive_line)
utils.remove_all_implicit_info(mline)
del mline['tree']
mline['unique_ids'] = [sfo['name']]
mline['seqs'] = [
sfo['seq']
] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['input_seqs'] = [
sfo['seq']
] # it's really important to set both the seqs (since they're both already in there from the naive line)
reco_info[sfo['name']] = mline
utils.add_implicit_info(glfo, mline)
final_line = utils.synthesize_multi_seq_line_from_reco_info(
[sfo['name'] for sfo in seqfos], reco_info)
if args.debug:
utils.print_reco_event(final_line)
# extract kd values from pickle file (use a separate script since it requires ete/anaconda to read)
if args.stype == 'selection':
cmd = 'export PATH=%s:$PATH && xvfb-run -a python ./bin/view-trees.py --pickle-tree-file %s/%s_lineage_tree.p --kdfile %s/kd-vals.csv --newick-tree-file %s/simu.nwk' % (
ete_path, outdir, args.extrastr, outdir, outdir)
utils.simplerun(cmd, shell=True)
kdvals = {}
with open('%s/kd-vals.csv' % outdir) as kdfile:
reader = csv.DictReader(kdfile)
for line in reader:
kdvals[line['uid']] = float(line['kd'])
if len(
set(kdvals) - set(final_line['unique_ids'])
) > 0: # uids in the kd file but not the <line> (i.e. not in the newick/fasta files) are probably just bcr-phylo discarding internal nodes
print ' in kd file, but missing from final_line (probably just internal nodes that bcr-phylo wrote to the tree without names): %s' % (
set(kdvals) - set(final_line['unique_ids']))
if len(set(final_line['unique_ids']) - set(kdvals)) > 0:
print ' in final_line, but missing from kdvals: %s' % ' '.join(
set(final_line['unique_ids']) - set(kdvals))
final_line['affinities'] = [
1. / kdvals[u] for u in final_line['unique_ids']
]
tree = treeutils.get_dendro_tree(treefname='%s/simu.nwk' % outdir)
if args.debug:
print utils.pad_lines(treeutils.get_ascii_tree(dendro_tree=tree),
padwidth=12)
final_line['tree'] = tree.as_string(schema='newick')
tmp_event = RecombinationEvent(
glfo) # I don't want to move the function out of event.py right now
tmp_event.set_reco_id(
final_line, irandom=ievent
) # not sure that setting <irandom> here actually does anything
# get target sequences
target_seqfos = utils.read_fastx('%s/%s_targets.fa' %
(outdir, args.extrastr))
final_line['target_seqs'] = [tfo['seq'] for tfo in target_seqfos]
from Bio.Seq import Seq
final_line['nearest_target_indices'] = []
aa_targets = [Seq(seq).translate() for seq in final_line['target_seqs']]
for mseq in final_line['input_seqs']:
aa_mseq = Seq(mseq).translate()
aa_hdists = [
utils.hamming_distance(aa_t, aa_mseq, amino_acid=True)
for aa_t in aa_targets
]
imin = aa_hdists.index(
min(aa_hdists)
) # NOTE doesn't do anything differently if there's more than one min
final_line['nearest_target_indices'].append(imin)
return final_line
def parse_bcr_phylo_output(glfo, naive_line, outdir, ievent):
seqfos = utils.read_fastx(bcr_phylo_fasta_fname(outdir)) # output mutated sequences from bcr-phylo
assert len(naive_line['unique_ids']) == 1 # enforces that we ran naive-only, 1-leaf partis simulation above
assert not indelutils.has_indels(naive_line['indelfos'][0]) # would have to handle this below
if args.debug:
utils.print_reco_event(naive_line)
reco_info = collections.OrderedDict()
for sfo in seqfos:
mline = copy.deepcopy(naive_line)
utils.remove_all_implicit_info(mline)
del mline['tree']
mline['unique_ids'] = [sfo['name']]
mline['seqs'] = [sfo['seq']] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['input_seqs'] = [sfo['seq']] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['duplicates'] = [[]]
reco_info[sfo['name']] = mline
try:
utils.add_implicit_info(glfo, mline)
except: # TODO not sure if I really want to leave this in long term, but it shouldn't hurt anything (it's crashing on unequal naive/mature sequence lengths, and I need this to track down which event it is) UPDATE: yeah it was just because something crashed in the middle of writing a .fa file
print 'implicit info adding failed for ievent %d in %s' % (ievent, outdir)
lines = traceback.format_exception(*sys.exc_info())
print utils.pad_lines(''.join(lines)) # NOTE this will still crash on the next line if implicit info adding failed
final_line = utils.synthesize_multi_seq_line_from_reco_info([sfo['name'] for sfo in seqfos], reco_info)
if args.debug:
utils.print_reco_event(final_line)
# extract kd values from pickle file (use a separate script since it requires ete/anaconda to read)
if args.stype == 'selection':
kdfname, nwkfname = '%s/kd-vals.csv' % outdir, '%s/simu.nwk' % outdir
if not utils.output_exists(args, kdfname, outlabel='kd/nwk conversion', offset=4): # eh, don't really need to check for both kd an nwk file, chances of only one being missing are really small, and it'll just crash when it looks for it a couple lines later
cmd = './bin/read-bcr-phylo-trees.py --pickle-tree-file %s/%s_lineage_tree.p --kdfile %s --newick-tree-file %s' % (outdir, args.extrastr, kdfname, nwkfname)
utils.run_ete_script(cmd, ete_path, debug=args.n_procs==1)
nodefo = {}
with open(kdfname) as kdfile:
reader = csv.DictReader(kdfile)
for line in reader:
nodefo[line['uid']] = {
'kd' : float(line['kd']),
'relative_kd' : float(line['relative_kd']),
'lambda' : line.get('lambda', None),
'target_index' : int(line['target_index']),
}
if len(set(nodefo) - set(final_line['unique_ids'])) > 0: # uids in the kd file but not the <line> (i.e. not in the newick/fasta files) are probably just bcr-phylo discarding internal nodes
print ' in kd file, but missing from final_line (probably just internal nodes that bcr-phylo wrote to the tree without names): %s' % (set(nodefo) - set(final_line['unique_ids']))
if len(set(final_line['unique_ids']) - set(nodefo)) > 0:
print ' in final_line, but missing from kdvals: %s' % ' '.join(set(final_line['unique_ids']) - set(nodefo))
final_line['affinities'] = [1. / nodefo[u]['kd'] for u in final_line['unique_ids']]
final_line['relative_affinities'] = [1. / nodefo[u]['relative_kd'] for u in final_line['unique_ids']]
final_line['lambdas'] = [nodefo[u]['lambda'] for u in final_line['unique_ids']]
final_line['nearest_target_indices'] = [nodefo[u]['target_index'] for u in final_line['unique_ids']]
tree = treeutils.get_dendro_tree(treefname=nwkfname)
tree.scale_edges(1. / numpy.mean([len(s) for s in final_line['seqs']]))
if args.debug:
print utils.pad_lines(treeutils.get_ascii_tree(dendro_tree=tree), padwidth=12)
final_line['tree'] = tree.as_string(schema='newick')
tmp_event = RecombinationEvent(glfo) # I don't want to move the function out of event.py right now
tmp_event.set_reco_id(final_line, irandom=ievent) # not sure that setting <irandom> here actually does anything
# get target sequences
target_seqfos = utils.read_fastx('%s/%s_targets.fa' % (outdir, args.extrastr))
final_line['target_seqs'] = [tfo['seq'] for tfo in target_seqfos]
return final_line
def get_mature_line(sfos,
naive_line,
glfo,
nodefo,
dtree,
target_sfos,
locus=None):
assert len(
naive_line['unique_ids']
) == 1 # enforces that we ran naive-only, 1-leaf partis simulation above
assert not indelutils.has_indels(
naive_line['indelfos'][0]) # would have to handle this below
if args.debug:
utils.print_reco_event(naive_line)
reco_info = collections.OrderedDict()
for sfo in sfos:
mline = utils.get_non_implicit_copy(naive_line)
del mline['tree']
mline['unique_ids'] = [sfo['name']]
mline['seqs'] = [sfo['seq']]
mline['input_seqs'] = [
sfo['seq']
] # it's really important to set both the seqs (since they're both already in there from the naive line)
mline['duplicates'] = [[]]
reco_info[sfo['name']] = mline
try:
utils.add_implicit_info(glfo, mline)
except: # TODO not sure if I really want to leave this in long term, but it shouldn't hurt anything (it's crashing on unequal naive/mature sequence lengths, and I need this to track down which event it is) UPDATE: yeah it was just because something crashed in the middle of writing a .fa file
print 'implicit info adding failed for ievent %d in %s' % (
ievent, outdir)
lines = traceback.format_exception(*sys.exc_info())
print utils.pad_lines(
''.join(lines)
) # NOTE this will still crash on the next line if implicit info adding failed
final_line = utils.synthesize_multi_seq_line_from_reco_info(
[sfo['name'] for sfo in sfos], reco_info)
ftree = copy.deepcopy(dtree)
if locus is not None:
def ltr(u):
return u + '-' + locus
new_nodefo = {}
for u_old in nodefo:
new_nodefo[ltr(u_old)] = nodefo[u_old]
nodefo = new_nodefo
treeutils.translate_labels(ftree,
[(u, ltr(u))
for u in final_line['unique_ids']])
final_line['unique_ids'] = [
ltr(u) for u in final_line['unique_ids']
]
assert len(sfos) == len(final_line['unique_ids'])
for iseq, sfo in enumerate(sfos):
naive_id = naive_line['unique_ids'][0]
assert naive_id.count('-') == 1
bstr = naive_id.replace('-' + locus, '')
pids = final_line['paired-uids'][iseq]
assert len(pids) == 1 and pids[0].find(
bstr
) == 0 and pids[0].count('-') == 1 and pids[0].split(
'-'
)[1] in utils.loci # if uid is xxx-igh, paired id shoud be e.g. xxx-igk
final_line['paired-uids'][iseq] = [
p.replace(bstr, sfo['name']) for p in pids
]
if args.debug:
utils.print_reco_event(final_line)
# extract kd values from pickle file (use a separate script since it requires ete/anaconda to read)
if len(
set(nodefo) - set(final_line['unique_ids'])
) > 0: # uids in the kd file but not the <line> (i.e. not in the newick/fasta files) are probably just bcr-phylo discarding internal nodes
print ' in kd file, but missing from final_line (probably just internal nodes that bcr-phylo wrote to the tree without names): %s' % (
set(nodefo) - set(final_line['unique_ids']))
if len(set(final_line['unique_ids']) - set(nodefo)) > 0:
print ' in final_line, but missing from kdvals: %s' % ' '.join(
set(final_line['unique_ids']) - set(nodefo))
final_line['affinities'] = [
1. / nodefo[u]['kd'] for u in final_line['unique_ids']
]
final_line['relative_affinities'] = [
1. / nodefo[u]['relative_kd'] for u in final_line['unique_ids']
]
final_line['lambdas'] = [
nodefo[u]['lambda'] for u in final_line['unique_ids']
]
final_line['nearest_target_indices'] = [
nodefo[u]['target_index'] for u in final_line['unique_ids']
]
ftree.scale_edges(1. / numpy.mean([len(s)
for s in final_line['seqs']]))
if args.debug:
print utils.pad_lines(treeutils.get_ascii_tree(dendro_tree=ftree),
padwidth=12)
final_line['tree'] = ftree.as_string(schema='newick')
tmp_event = RecombinationEvent(
glfo
) # I don't want to move the function out of event.py right now
tmp_event.set_reco_id(
final_line, irandom=ievent
) # not sure that setting <irandom> here actually does anything
final_line['target_seqs'] = [tfo['seq'] for tfo in target_sfos]
return final_line
