args = parser.parse_args()
args.extra_columns = utils.get_arg_list(args.extra_columns)
assert utils.getsuffix(args.outfile) in ['.csv', '.tsv', '.fa', '.fasta']
default_glfo_dir = partis_dir + '/data/germlines/human'
if utils.getsuffix(args.infile) == '.csv' and args.glfo_dir is None:
print ' note: reading deprecated csv format, so need to get germline info from a separate directory; --glfo-dir was not set, so using default %s. If it doesn\'t crash, it\'s probably ok.' % default_glfo_dir
args.glfo_dir = default_glfo_dir
glfo, annotation_list, cpath = utils.read_output(args.infile, glfo_dir=args.glfo_dir, locus=args.locus)
if args.plotdir is not None:
from parametercounter import ParameterCounter
setattr(args, 'region_end_exclusions', {r : [0 for e in ['5p', '3p']] for r in utils.regions}) # hackity hackity hackity
pcounter = ParameterCounter(glfo, args)
for line in annotation_list:
pcounter.increment(line)
pcounter.plot(args.plotdir) #, make_per_base_plots=True) #, only_overall=True, make_per_base_plots=True
sys.exit(0)
if cpath is None or cpath.i_best is None:
clusters_to_use = [l['unique_ids'] for l in annotation_list]
print ' no cluster path in input file, so just using all %d sequences (in %d clusters) in annotations' % (sum(len(c) for c in clusters_to_use), len(clusters_to_use))
else:
ipartition = cpath.i_best if args.partition_index is None else args.partition_index
print ' found %d clusters in %s' % (len(cpath.partitions[ipartition]), 'best partition' if args.partition_index is None else 'partition at index %d (of %d)' % (ipartition, len(cpath.partitions)))
if args.cluster_index is None:
clusters_to_use = cpath.partitions[ipartition]
print ' taking all %d clusters' % len(clusters_to_use)
else:
clusters_to_use = [cpath.partitions[ipartition][args.cluster_index]]
print ' taking cluster at index %d with size %d' % (args.cluster_index, len(clusters_to_use[0]))
def read_hmm_output(self,
algorithm,
hmm_csv_outfname,
make_clusters=True,
count_parameters=False,
parameter_out_dir=None,
plotdir=None):
print ' read output'
if count_parameters:
assert parameter_out_dir is not None
assert plotdir is not None
pcounter = ParameterCounter(
self.germline_seqs) if count_parameters else None
true_pcounter = ParameterCounter(self.germline_seqs) if (
count_parameters and not self.args.is_data) else None
perfplotter = PerformancePlotter(
self.germline_seqs, plotdir +
'/hmm/performance', 'hmm') if self.args.plot_performance else None
n_processed = 0
hmminfo = []
with opener('r')(hmm_csv_outfname) as hmm_csv_outfile:
reader = csv.DictReader(hmm_csv_outfile)
last_key = None
boundary_error_queries = []
for line in reader:
utils.intify(line, splitargs=('unique_ids', 'seqs'))
ids = line['unique_ids']
this_key = utils.get_key(ids)
same_event = from_same_event(self.args.is_data, True,
self.reco_info, ids)
id_str = ''.join(['%20s ' % i for i in ids])
# check for errors
if last_key != this_key: # if this is the first line for this set of ids (i.e. the best viterbi path or only forward score)
if line['errors'] != None and 'boundary' in line[
'errors'].split(':'):
boundary_error_queries.append(':'.join(
[str(uid) for uid in ids]))
else:
assert len(line['errors']) == 0
if algorithm == 'viterbi':
line['seq'] = line['seqs'][
0] # add info for the best match as 'seq'
line['unique_id'] = ids[0]
utils.add_match_info(self.germline_seqs,
line,
self.cyst_positions,
self.tryp_positions,
debug=(self.args.debug > 0))
if last_key != this_key or self.args.plot_all_best_events: # if this is the first line (i.e. the best viterbi path) for this query (or query pair), print the true event
n_processed += 1
if self.args.debug:
print '%s %d' % (id_str, same_event)
if line['cdr3_length'] != -1 or not self.args.skip_unproductive: # if it's productive, or if we're not skipping unproductive rearrangements
hmminfo.append(
dict([
('unique_id', line['unique_ids'][0]),
] + line.items()))
if pcounter is not None: # increment counters (but only for the best [first] match)
pcounter.increment(line)
if true_pcounter is not None: # increment true counters
true_pcounter.increment(self.reco_info[ids[0]])
if perfplotter is not None:
perfplotter.evaluate(self.reco_info[ids[0]],
line)
if self.args.debug:
self.print_hmm_output(
line,
print_true=(last_key != this_key),
perfplotter=perfplotter)
line['seq'] = None
line['unique_id'] = None
else: # for forward, write the pair scores to file to be read by the clusterer
if not make_clusters: # self.args.debug or
print '%3d %10.3f %s' % (
same_event, float(line['score']), id_str)
if line['score'] == '-nan':
print ' WARNING encountered -nan, setting to -999999.0'
score = -999999.0
else:
score = float(line['score'])
if len(ids) == 2:
hmminfo.append({
'id_a': line['unique_ids'][0],
'id_b': line['unique_ids'][1],
'score': score
})
n_processed += 1
last_key = utils.get_key(ids)
if pcounter is not None:
pcounter.write(parameter_out_dir)
if not self.args.no_plot:
pcounter.plot(plotdir,
subset_by_gene=True,
cyst_positions=self.cyst_positions,
tryp_positions=self.tryp_positions)
if true_pcounter is not None:
true_pcounter.write(parameter_out_dir + '/true')
if not self.args.no_plot:
true_pcounter.plot(plotdir + '/true',
subset_by_gene=True,
cyst_positions=self.cyst_positions,
tryp_positions=self.tryp_positions)
if perfplotter is not None:
perfplotter.plot()
print ' processed %d queries' % n_processed
if len(boundary_error_queries) > 0:
print ' %d boundary errors (%s)' % (
len(boundary_error_queries), ', '.join(boundary_error_queries))
return hmminfo
class Waterer(object):
""" Run smith-waterman on the query sequences in <infname> """
def __init__(self, args, input_info, reco_info, germline_seqs, parameter_dir, write_parameters=False, plotdir=None):
self.parameter_dir = parameter_dir
self.plotdir = plotdir
self.args = args
self.input_info = input_info
self.reco_info = reco_info
self.germline_seqs = germline_seqs
self.pcounter, self.true_pcounter = None, None
if write_parameters:
self.pcounter = ParameterCounter(self.germline_seqs)
if not self.args.is_data:
self.true_pcounter = ParameterCounter(self.germline_seqs)
self.info = {}
self.info['all_best_matches'] = set() # set of all the matches we found (for *all* queries)
self.info['skipped_unproductive_queries'] = [] # list of unproductive queries
if self.args.apply_choice_probs_in_sw:
if self.args.debug:
print ' reading gene choice probs from',parameter_dir
self.gene_choice_probs = utils.read_overall_gene_probs(parameter_dir)
with opener('r')(self.args.datadir + '/v-meta.json') as json_file: # get location of <begin> cysteine in each v region
self.cyst_positions = json.load(json_file)
with opener('r')(self.args.datadir + '/j_tryp.csv') as csv_file: # get location of <end> tryptophan in each j region (TGG)
tryp_reader = csv.reader(csv_file)
self.tryp_positions = {row[0]:row[1] for row in tryp_reader} # WARNING: this doesn't filter out the header line
self.outfile = None
if self.args.outfname != None:
self.outfile = open(self.args.outfname, 'a')
self.n_unproductive = 0
self.n_total = 0
# ----------------------------------------------------------------------------------------
def __del__(self):
if self.args.outfname != None:
self.outfile.close()
# ----------------------------------------------------------------------------------------
def clean(self):
if self.pcounter != None:
self.pcounter.clean()
if self.true_pcounter != None:
self.true_pcounter.clean()
# ----------------------------------------------------------------------------------------
def run(self):
start = time.time()
base_infname = 'query-seqs.fa'
base_outfname = 'query-seqs.bam'
sys.stdout.flush()
self.write_vdjalign_input(base_infname)
if self.args.n_procs == 1:
cmd_str = self.get_vdjalign_cmd_str(self.args.workdir, base_infname, base_outfname)
check_call(cmd_str.split())
if not self.args.no_clean:
os.remove(self.args.workdir + '/' + base_infname)
else:
procs = []
for iproc in range(self.args.n_procs):
cmd_str = self.get_vdjalign_cmd_str(self.args.workdir + '/sw-' + str(iproc), base_infname, base_outfname, iproc)
procs.append(Popen(cmd_str.split()))
time.sleep(0.1)
for proc in procs:
proc.wait()
if not self.args.no_clean:
for iproc in range(self.args.n_procs):
os.remove(self.args.workdir + '/sw-' + str(iproc) + '/' + base_infname)
sys.stdout.flush()
self.read_output(base_outfname, plot_performance=self.args.plot_performance)
print ' sw time: %.3f' % (time.time()-start)
if self.n_unproductive > 0:
print ' unproductive skipped %d / %d = %.2f' % (self.n_unproductive, self.n_total, float(self.n_unproductive) / self.n_total)
if self.pcounter != None:
self.pcounter.write(self.parameter_dir)
# if self.true_pcounter != None:
# self.true_pcounter.write(parameter_xxx_dir, plotdir=plotdir + '/true')
if not self.args.no_plot and self.plotdir != '':
self.pcounter.plot(self.plotdir, subset_by_gene=True, cyst_positions=self.cyst_positions, tryp_positions=self.tryp_positions)
if self.true_pcounter != None:
self.true_pcounter.plot(self.plotdir + '/true', subset_by_gene=True, cyst_positions=self.cyst_positions, tryp_positions=self.tryp_positions)
# ----------------------------------------------------------------------------------------
def write_vdjalign_input(self, base_infname):
# first make a list of query names so we can iterate over an ordered collection
ordered_info = []
for query_name in self.input_info:
ordered_info.append(query_name)
queries_per_proc = float(len(self.input_info)) / self.args.n_procs
n_queries_per_proc = int(math.ceil(queries_per_proc))
if self.args.n_procs == 1: # double check for rounding problems or whatnot
assert n_queries_per_proc == len(self.input_info)
for iproc in range(self.args.n_procs):
workdir = self.args.workdir
if self.args.n_procs > 1:
workdir += '/sw-' + str(iproc)
utils.prep_dir(workdir)
infname = workdir + '/' + base_infname
with opener('w')(workdir + '/' + base_infname) as sub_infile:
for iquery in range(iproc*n_queries_per_proc, (iproc + 1)*n_queries_per_proc):
if iquery >= len(ordered_info):
break
query_name = ordered_info[iquery]
sub_infile.write('>' + str(query_name) + ' NUKES\n')
sub_infile.write(self.input_info[query_name]['seq'] + '\n')
# ----------------------------------------------------------------------------------------
def get_vdjalign_cmd_str(self, workdir, base_infname, base_outfname, iproc=-1):
"""
Run smith-waterman alignment (from Connor's ighutils package) on the seqs in <base_infname>, and toss all the top matches into <base_outfname>.
"""
# large gap-opening penalty: we want *no* gaps in the middle of the alignments
# match score larger than (negative) mismatch score: we want to *encourage* some level of shm. If they're equal, we tend to end up with short unmutated alignments, which screws everything up
os.environ['PATH'] = os.getenv('PWD') + '/packages/samtools:' + os.getenv('PATH')
check_output(['which', 'samtools'])
cmd_str = self.args.ighutil_dir + '/bin/vdjalign align-fastq -q'
if self.args.slurm:
cmd_str = 'srun ' + cmd_str
cmd_str += ' --max-drop 50'
cmd_str += ' --match 5 --mismatch 3'
cmd_str += ' --gap-open 1000'
cmd_str += ' --vdj-dir ' + self.args.datadir
cmd_str += ' ' + workdir + '/' + base_infname + ' ' + workdir + '/' + base_outfname
return cmd_str
# ----------------------------------------------------------------------------------------
def read_output(self, base_outfname, plot_performance=False):
perfplotter = None
if plot_performance:
assert self.args.plotdir != None
assert not self.args.is_data
from performanceplotter import PerformancePlotter
perfplotter = PerformancePlotter(self.germline_seqs, self.args.plotdir + '/sw/performance', 'sw')
n_processed = 0
for iproc in range(self.args.n_procs):
workdir = self.args.workdir
if self.args.n_procs > 1:
workdir += '/sw-' + str(iproc)
outfname = workdir + '/' + base_outfname
with contextlib.closing(pysam.Samfile(outfname)) as bam:
grouped = itertools.groupby(iter(bam), operator.attrgetter('qname'))
for _, reads in grouped: # loop over query sequences
self.n_total += 1
self.process_query(bam, list(reads), perfplotter)
n_processed += 1
if not self.args.no_clean:
os.remove(outfname)
if self.args.n_procs > 1: # still need the top-level workdir
os.rmdir(workdir)
print ' processed %d queries' % n_processed
if perfplotter != None:
perfplotter.plot()
# ----------------------------------------------------------------------------------------
def get_choice_prob(self, region, gene):
choice_prob = 1.0
if gene in self.gene_choice_probs[region]:
choice_prob = self.gene_choice_probs[region][gene]
else:
choice_prob = 0.0 # NOTE would it make sense to use something else here?
return choice_prob
# ----------------------------------------------------------------------------------------
def process_query(self, bam, reads, perfplotter=None):
primary = next((r for r in reads if not r.is_secondary), None)
query_seq = primary.seq
try:
query_name = int(primary.qname) # if it's just one of my hashes, we want it as an int
except ValueError:
query_name = primary.qname # but if it's someone else's random-ass alphasymbolonumeric string we'll just leave it as-is
raw_best = {}
all_match_names = {}
warnings = {} # ick, this is a messy way to pass stuff around
for region in utils.regions:
all_match_names[region] = []
all_query_bounds, all_germline_bounds = {}, {}
for read in reads: # loop over the matches found for each query sequence
read.seq = query_seq # only the first one has read.seq set by default, so we need to set the rest by hand
gene = bam.references[read.tid]
region = utils.get_region(gene)
warnings[gene] = ''
if region not in raw_best: # best v, d, and j before multiplying by gene choice probs. needed 'cause *these* are the v and j that get excised
raw_best[region] = gene
raw_score = read.tags[0][1] # raw because they don't include the gene choice probs
score = raw_score
if self.args.apply_choice_probs_in_sw: # NOTE I stopped applying the gene choice probs here because the smith-waterman scores don't correspond to log-probs, so throwing on the gene choice probs was dubious (and didn't seem to work that well)
score = self.get_choice_prob(region, gene) * raw_score # multiply by the probability to choose this gene
# set bounds
qrbounds = (read.qstart, read.qend)
glbounds = (read.pos, read.aend)
assert qrbounds[1]-qrbounds[0] == glbounds[1]-glbounds[0]
assert qrbounds[1] <= len(query_seq)
if glbounds[1] > len(self.germline_seqs[region][gene]):
print ' ', gene
print ' ', glbounds[1], len(self.germline_seqs[region][gene])
print ' ', self.germline_seqs[region][gene]
assert glbounds[1] <= len(self.germline_seqs[region][gene])
assert qrbounds[1]-qrbounds[0] == glbounds[1]-glbounds[0]
all_match_names[region].append((score,gene)) # NOTE it is important that this is ordered such that the best match is first
all_query_bounds[gene] = qrbounds
all_germline_bounds[gene] = glbounds
self.summarize_query(query_name, query_seq, raw_best, all_match_names, all_query_bounds, all_germline_bounds, perfplotter, warnings)
# ----------------------------------------------------------------------------------------
def print_match(self, region, gene, query_seq, score, glbounds, qrbounds, codon_pos, warnings, skipping=False):
if self.args.debug < 2:
return
out_str_list = []
buff_str = (20 - len(gene)) * ' '
tmp_val = score
if self.args.apply_choice_probs_in_sw and self.get_choice_prob(region, gene) != 0.0:
tmp_val = score / self.get_choice_prob(region, gene)
if self.args.apply_choice_probs_in_sw:
out_str_list.append('%8s%s%s%9.1e * %3.0f = %-6.1f' % (' ', utils.color_gene(gene), buff_str, self.get_choice_prob(region, gene), tmp_val, score))
else:
out_str_list.append('%8s%s%s%9s%3s %6.0f ' % (' ', utils.color_gene(gene), '', '', buff_str, score))
out_str_list.append('%4d%4d %s\n' % (glbounds[0], glbounds[1], self.germline_seqs[region][gene][glbounds[0]:glbounds[1]]))
out_str_list.append('%50s %4d%4d' % ('', qrbounds[0], qrbounds[1]))
out_str_list.append(' %s ' % (utils.color_mutants(self.germline_seqs[region][gene][glbounds[0]:glbounds[1]], query_seq[qrbounds[0]:qrbounds[1]])))
if region != 'd':
out_str_list.append('(%s %d)' % (utils.conserved_codon_names[region], codon_pos))
if warnings[gene] != '':
out_str_list.append('WARNING ' + warnings[gene])
if skipping:
out_str_list.append('skipping!')
if self.args.outfname == None:
print ''.join(out_str_list)
else:
out_str_list.append('\n')
self.outfile.write(''.join(out_str_list))
# ----------------------------------------------------------------------------------------
def shift_overlapping_boundaries(self, qrbounds, glbounds, query_name, query_seq, best):
# NOTE this does pretty much the same thing as resolve_overlapping_matches in joinparser.py
""" s-w allows d and j matches (and v and d matches) to overlap... which makes no sense, so apportion the disputed territory between the two regions """
for region_pairs in ({'left':'v', 'right':'d'}, {'left':'d', 'right':'j'}):
l_reg = region_pairs['left']
r_reg = region_pairs['right']
l_gene = best[l_reg]
r_gene = best[r_reg]
overlap = qrbounds[l_gene][1] - qrbounds[r_gene][0]
if overlap > 0:
l_length = qrbounds[l_gene][1] - qrbounds[l_gene][0]
r_length = qrbounds[r_gene][1] - qrbounds[r_gene][0]
l_portion, r_portion = 0, 0
while l_portion + r_portion < overlap:
if l_length <= 1 and r_length <= 1: # don't want to erode match (in practice it'll be the d match) all the way to zero
print ' ERROR both lengths went to zero'
assert False
elif l_length > 1 and r_length > 1: # if both have length left, alternate back and forth
if (l_portion + r_portion) % 2 == 0:
l_portion += 1 # give one base to the left
l_length -= 1
else:
r_portion += 1 # and one to the right
r_length -= 1
elif l_length > 1:
l_portion += 1
l_length -= 1
elif r_length > 1:
r_portion += 1
r_length -= 1
if self.args.debug:
print ' WARNING %s apportioning %d bases between %s (%d) match and %s (%d) match' % (str(query_name), overlap, l_reg, l_portion, r_reg, r_portion)
assert l_portion + r_portion == overlap
qrbounds[l_gene] = (qrbounds[l_gene][0], qrbounds[l_gene][1] - l_portion)
glbounds[l_gene] = (glbounds[l_gene][0], glbounds[l_gene][1] - l_portion)
qrbounds[r_gene] = (qrbounds[r_gene][0] + r_portion, qrbounds[r_gene][1])
glbounds[r_gene] = (glbounds[r_gene][0] + r_portion, glbounds[r_gene][1])
best[l_reg + '_gl_seq'] = self.germline_seqs[l_reg][l_gene][glbounds[l_gene][0] : glbounds[l_gene][1]]
best[l_reg + '_qr_seq'] = query_seq[qrbounds[l_gene][0]:qrbounds[l_gene][1]]
best[r_reg + '_gl_seq'] = self.germline_seqs[r_reg][r_gene][glbounds[r_gene][0] : glbounds[r_gene][1]]
best[r_reg + '_qr_seq'] = query_seq[qrbounds[r_gene][0]:qrbounds[r_gene][1]]
# ----------------------------------------------------------------------------------------
def add_to_info(self, query_name, query_seq, kvals, match_names, best, all_germline_bounds, all_query_bounds, codon_positions, perfplotter=None):
assert query_name not in self.info
self.info[query_name] = {}
self.info[query_name]['unique_id'] = query_name # redundant, but used somewhere down the line
self.info[query_name]['k_v'] = kvals['v']
self.info[query_name]['k_d'] = kvals['d']
self.info[query_name]['all'] = ':'.join(match_names['v'] + match_names['d'] + match_names['j'])
assert codon_positions['v'] != -1
assert codon_positions['j'] != -1
self.info[query_name]['cdr3_length'] = codon_positions['j'] - codon_positions['v'] + 3 #tryp_position_in_joined_seq - self.cyst_position + 3
self.info[query_name]['cyst_position'] = codon_positions['v']
self.info[query_name]['tryp_position'] = codon_positions['j']
# erosion, insertion, mutation info for best match
self.info[query_name]['v_5p_del'] = all_germline_bounds[best['v']][0]
self.info[query_name]['v_3p_del'] = len(self.germline_seqs['v'][best['v']]) - all_germline_bounds[best['v']][1] # len(germline v) - gl_match_end
self.info[query_name]['d_5p_del'] = all_germline_bounds[best['d']][0]
self.info[query_name]['d_3p_del'] = len(self.germline_seqs['d'][best['d']]) - all_germline_bounds[best['d']][1]
self.info[query_name]['j_5p_del'] = all_germline_bounds[best['j']][0]
self.info[query_name]['j_3p_del'] = len(self.germline_seqs['j'][best['j']]) - all_germline_bounds[best['j']][1]
self.info[query_name]['fv_insertion'] = query_seq[ : all_query_bounds[best['v']][0]]
self.info[query_name]['vd_insertion'] = query_seq[all_query_bounds[best['v']][1] : all_query_bounds[best['d']][0]]
self.info[query_name]['dj_insertion'] = query_seq[all_query_bounds[best['d']][1] : all_query_bounds[best['j']][0]]
self.info[query_name]['jf_insertion'] = query_seq[all_query_bounds[best['j']][1] : ]
for region in utils.regions:
self.info[query_name][region + '_gene'] = best[region]
self.info[query_name][region + '_gl_seq'] = best[region + '_gl_seq']
self.info[query_name][region + '_qr_seq'] = best[region + '_qr_seq']
self.info['all_best_matches'].add(best[region])
self.info[query_name]['seq'] = query_seq # only need to add this so I can pass it to print_reco_event
if self.args.debug:
if not self.args.is_data:
utils.print_reco_event(self.germline_seqs, self.reco_info[query_name], extra_str=' ', label='true:')
utils.print_reco_event(self.germline_seqs, self.info[query_name], extra_str=' ', label='inferred:')
if self.pcounter != None:
self.pcounter.increment(self.info[query_name])
if self.true_pcounter != None:
self.true_pcounter.increment(self.reco_info[query_name])
if perfplotter != None:
perfplotter.evaluate(self.reco_info[query_name], self.info[query_name]) #, subtract_unphysical_erosions=True)
# ----------------------------------------------------------------------------------------
def summarize_query(self, query_name, query_seq, raw_best, all_match_names, all_query_bounds, all_germline_bounds, perfplotter, warnings):
if self.args.debug:
print '%s' % str(query_name)
best, match_names, n_matches = {}, {}, {}
n_used = {'v':0, 'd':0, 'j':0}
k_v_min, k_d_min = 999, 999
k_v_max, k_d_max = 0, 0
for region in utils.regions:
all_match_names[region] = sorted(all_match_names[region], reverse=True)
match_names[region] = []
codon_positions = {'v':-1, 'd':-1, 'j':-1} # conserved codon positions (v:cysteine, d:dummy, j:tryptophan)
for region in utils.regions:
n_matches[region] = len(all_match_names[region])
n_skipped = 0
for score, gene in all_match_names[region]:
glbounds = all_germline_bounds[gene]
qrbounds = all_query_bounds[gene]
assert qrbounds[1] <= len(query_seq) # NOTE I'm putting these up avove as well (in process_query), so in time I should remove them from here
assert glbounds[1] <= len(self.germline_seqs[region][gene])
assert qrbounds[0] >= 0
assert glbounds[0] >= 0
glmatchseq = self.germline_seqs[region][gene][glbounds[0]:glbounds[1]]
# only use the best few matches
if n_used[region] >= int(self.args.n_max_per_region[utils.regions.index(region)]): # only take the top few from each region
break
# only use a specified set of genes
if self.args.only_genes != None and gene not in self.args.only_genes:
n_skipped += 1
continue
# add match to the list
n_used[region] += 1
match_names[region].append(gene)
self.print_match(region, gene, query_seq, score, glbounds, qrbounds, -1, warnings, skipping=False)
# if the germline match and the query match aren't the same length, s-w likely added an insert, which we shouldn't get since the gap-open penalty is jacked up so high
if len(glmatchseq) != len(query_seq[qrbounds[0]:qrbounds[1]]): # neurotic double check (um, I think) EDIT hey this totally saved my ass
print 'ERROR %d not same length' % query_name
print glmatchseq, glbounds[0], glbounds[1]
print query_seq[qrbounds[0]:qrbounds[1]]
assert False
if region == 'v':
this_k_v = all_query_bounds[gene][1] # NOTE even if the v match doesn't start at the left hand edge of the query sequence, we still measure k_v from there.
# In other words, sw doesn't tell the hmm about it
k_v_min = min(this_k_v, k_v_min)
k_v_max = max(this_k_v, k_v_max)
if region == 'd':
this_k_d = all_query_bounds[gene][1] - all_query_bounds[raw_best['v']][1] # end of d minus end of v
k_d_min = min(this_k_d, k_d_min)
k_d_max = max(this_k_d, k_d_max)
# check consistency with best match (since the best match is excised in s-w code, and because ham is run with *one* k_v k_d set)
if region not in best:
best[region] = gene
best[region + '_gl_seq'] = self.germline_seqs[region][gene][glbounds[0]:glbounds[1]]
best[region + '_qr_seq'] = query_seq[qrbounds[0]:qrbounds[1]]
best[region + '_score'] = score
if self.args.debug and n_skipped > 0:
print '%8s skipped %d %s genes' % ('', n_skipped, region)
for region in utils.regions:
if region not in best:
print ' no',region,'match found for',query_name # NOTE if no d match found, we should really should just assume entire d was eroded
if not self.args.is_data:
print ' true:'
utils.print_reco_event(self.germline_seqs, self.reco_info[query_name], extra_str=' ')
return
# s-w allows d and j matches to overlap... which makes no sense, so arbitrarily give the disputed territory to j
try:
self.shift_overlapping_boundaries(all_query_bounds, all_germline_bounds, query_name, query_seq, best)
except AssertionError:
print ' ERROR %s apportionment failed' % str(query_name)
return
for region in utils.regions:
codon_positions[region] = utils.get_conserved_codon_position(self.cyst_positions, self.tryp_positions, region, best[region], all_germline_bounds, all_query_bounds) # position in the query sequence, that is
# check for unproductive rearrangements
try:
# NOTE it's actually expected that this'll fail with a 'sequence too short' error, since the s-w doesn't know it's supposed to make sure the match contains the conserved codons
utils.check_both_conserved_codons(query_seq, codon_positions['v'], codon_positions['j'], debug=self.args.debug, extra_str=' ')
cdr3_length = codon_positions['j'] - codon_positions['v'] + 3
if cdr3_length % 3 != 0: # make sure we've stayed in frame
if self.args.debug:
print ' out of frame cdr3: %d %% 3 = %d' % (cdr3_length, cdr3_length % 3)
assert False
utils.check_for_stop_codon(query_seq, codon_positions['v'], debug=self.args.debug)
except AssertionError:
if self.args.debug:
print ' unproductive rearrangement in waterer'
if self.args.skip_unproductive:
if self.args.debug:
print ' ...skipping'
self.n_unproductive += 1
self.info['skipped_unproductive_queries'].append(query_name)
return
# best k_v, k_d:
k_v = all_query_bounds[best['v']][1] # end of v match
k_d = all_query_bounds[best['d']][1] - all_query_bounds[best['v']][1] # end of d minus end of v
if k_d_max < 5: # since the s-w step matches to the longest possible j and then excises it, this sometimes gobbles up the d, resulting in a very short d alignment.
if self.args.debug:
print ' expanding k_d'
k_d_max = max(8, k_d_max)
if 'IGHJ4*' in best['j'] and self.germline_seqs['d'][best['d']][-5:] == 'ACTAC': # the end of some d versions is the same as the start of some j versions, so the s-w frequently kicks out the 'wrong' alignment
if self.args.debug:
print ' doubly expanding k_d'
if k_d_max-k_d_min < 8:
k_d_min -= 5
k_d_max += 2
k_v_min = max(0, k_v_min - self.args.default_v_fuzz) # ok, so I don't *actually* want it to be zero... oh, well
k_v_max += self.args.default_v_fuzz
k_d_min = max(1, k_d_min - self.args.default_d_fuzz)
k_d_max += self.args.default_d_fuzz
assert k_v_min > 0 and k_d_min > 0 and k_v_max > 0 and k_d_max > 0
if self.args.debug:
print ' k_v: %d [%d-%d)' % (k_v, k_v_min, k_v_max)
print ' k_d: %d [%d-%d)' % (k_d, k_d_min, k_d_max)
print ' used',
for region in utils.regions:
print ' %s: %d/%d' % (region, n_used[region], n_matches[region]),
print ''
kvals = {}
kvals['v'] = {'best':k_v, 'min':k_v_min, 'max':k_v_max}
kvals['d'] = {'best':k_d, 'min':k_d_min, 'max':k_d_max}
self.add_to_info(query_name, query_seq, kvals, match_names, best, all_germline_bounds, all_query_bounds, codon_positions=codon_positions, perfplotter=perfplotter)
def read_hmm_output(self, algorithm, hmm_csv_outfname, make_clusters=True, count_parameters=False, parameter_out_dir=None, plotdir=None):
print ' read output'
if count_parameters:
assert parameter_out_dir is not None
assert plotdir is not None
pcounter = ParameterCounter(self.germline_seqs) if count_parameters else None
true_pcounter = ParameterCounter(self.germline_seqs) if (count_parameters and not self.args.is_data) else None
perfplotter = PerformancePlotter(self.germline_seqs, plotdir + '/hmm/performance', 'hmm') if self.args.plot_performance else None
n_processed = 0
hmminfo = []
with opener('r')(hmm_csv_outfname) as hmm_csv_outfile:
reader = csv.DictReader(hmm_csv_outfile)
last_key = None
boundary_error_queries = []
for line in reader:
utils.intify(line, splitargs=('unique_ids', 'seqs'))
ids = line['unique_ids']
this_key = utils.get_key(ids)
same_event = from_same_event(self.args.is_data, True, self.reco_info, ids)
id_str = ''.join(['%20s ' % i for i in ids])
# check for errors
if last_key != this_key: # if this is the first line for this set of ids (i.e. the best viterbi path or only forward score)
if line['errors'] != None and 'boundary' in line['errors'].split(':'):
boundary_error_queries.append(':'.join([str(uid) for uid in ids]))
else:
assert len(line['errors']) == 0
if algorithm == 'viterbi':
line['seq'] = line['seqs'][0] # add info for the best match as 'seq'
line['unique_id'] = ids[0]
utils.add_match_info(self.germline_seqs, line, self.cyst_positions, self.tryp_positions, debug=(self.args.debug > 0))
if last_key != this_key or self.args.plot_all_best_events: # if this is the first line (i.e. the best viterbi path) for this query (or query pair), print the true event
n_processed += 1
if self.args.debug:
print '%s %d' % (id_str, same_event)
if line['cdr3_length'] != -1 or not self.args.skip_unproductive: # if it's productive, or if we're not skipping unproductive rearrangements
hmminfo.append(dict([('unique_id', line['unique_ids'][0]), ] + line.items()))
if pcounter is not None: # increment counters (but only for the best [first] match)
pcounter.increment(line)
if true_pcounter is not None: # increment true counters
true_pcounter.increment(self.reco_info[ids[0]])
if perfplotter is not None:
perfplotter.evaluate(self.reco_info[ids[0]], line)
if self.args.debug:
self.print_hmm_output(line, print_true=(last_key != this_key), perfplotter=perfplotter)
line['seq'] = None
line['unique_id'] = None
else: # for forward, write the pair scores to file to be read by the clusterer
if not make_clusters: # self.args.debug or
print '%3d %10.3f %s' % (same_event, float(line['score']), id_str)
if line['score'] == '-nan':
print ' WARNING encountered -nan, setting to -999999.0'
score = -999999.0
else:
score = float(line['score'])
if len(ids) == 2:
hmminfo.append({'id_a':line['unique_ids'][0], 'id_b':line['unique_ids'][1], 'score':score})
n_processed += 1
last_key = utils.get_key(ids)
if pcounter is not None:
pcounter.write(parameter_out_dir)
if not self.args.no_plot:
pcounter.plot(plotdir, subset_by_gene=True, cyst_positions=self.cyst_positions, tryp_positions=self.tryp_positions)
if true_pcounter is not None:
true_pcounter.write(parameter_out_dir + '/true')
if not self.args.no_plot:
true_pcounter.plot(plotdir + '/true', subset_by_gene=True, cyst_positions=self.cyst_positions, tryp_positions=self.tryp_positions)
if perfplotter is not None:
perfplotter.plot()
print ' processed %d queries' % n_processed
if len(boundary_error_queries) > 0:
print ' %d boundary errors (%s)' % (len(boundary_error_queries), ', '.join(boundary_error_queries))
return hmminfo
class Waterer(object):
""" Run smith-waterman on the query sequences in <infname> """
def __init__(self,
args,
input_info,
reco_info,
germline_seqs,
parameter_dir,
write_parameters=False,
plotdir=None):
self.parameter_dir = parameter_dir
self.plotdir = plotdir
self.args = args
self.input_info = input_info
self.reco_info = reco_info
self.germline_seqs = germline_seqs
self.pcounter, self.true_pcounter = None, None
if write_parameters:
self.pcounter = ParameterCounter(self.germline_seqs)
if not self.args.is_data:
self.true_pcounter = ParameterCounter(self.germline_seqs)
self.info = {}
self.info['all_best_matches'] = set(
) # set of all the matches we found (for *all* queries)
self.info['skipped_unproductive_queries'] = [
] # list of unproductive queries
if self.args.apply_choice_probs_in_sw:
if self.args.debug:
print ' reading gene choice probs from', parameter_dir
self.gene_choice_probs = utils.read_overall_gene_probs(
parameter_dir)
with opener('r')(
self.args.datadir + '/v-meta.json'
) as json_file: # get location of <begin> cysteine in each v region
self.cyst_positions = json.load(json_file)
with opener('r')(
self.args.datadir + '/j_tryp.csv'
) as csv_file: # get location of <end> tryptophan in each j region (TGG)
tryp_reader = csv.reader(csv_file)
self.tryp_positions = {
row[0]: row[1]
for row in tryp_reader
} # WARNING: this doesn't filter out the header line
self.outfile = None
if self.args.outfname != None:
self.outfile = open(self.args.outfname, 'a')
self.n_unproductive = 0
self.n_total = 0
# ----------------------------------------------------------------------------------------
def __del__(self):
if self.args.outfname != None:
self.outfile.close()
# ----------------------------------------------------------------------------------------
def clean(self):
if self.pcounter != None:
self.pcounter.clean()
if self.true_pcounter != None:
self.true_pcounter.clean()
# ----------------------------------------------------------------------------------------
def run(self):
start = time.time()
base_infname = 'query-seqs.fa'
base_outfname = 'query-seqs.bam'
sys.stdout.flush()
self.write_vdjalign_input(base_infname)
if self.args.n_procs == 1:
cmd_str = self.get_vdjalign_cmd_str(self.args.workdir,
base_infname, base_outfname)
check_call(cmd_str.split())
if not self.args.no_clean:
os.remove(self.args.workdir + '/' + base_infname)
else:
procs = []
for iproc in range(self.args.n_procs):
cmd_str = self.get_vdjalign_cmd_str(
self.args.workdir + '/sw-' + str(iproc), base_infname,
base_outfname, iproc)
procs.append(Popen(cmd_str.split()))
time.sleep(0.1)
for proc in procs:
proc.wait()
if not self.args.no_clean:
for iproc in range(self.args.n_procs):
os.remove(self.args.workdir + '/sw-' + str(iproc) + '/' +
base_infname)
sys.stdout.flush()
self.read_output(base_outfname,
plot_performance=self.args.plot_performance)
print ' sw time: %.3f' % (time.time() - start)
if self.n_unproductive > 0:
print ' unproductive skipped %d / %d = %.2f' % (
self.n_unproductive, self.n_total,
float(self.n_unproductive) / self.n_total)
if self.pcounter != None:
self.pcounter.write(self.parameter_dir)
# if self.true_pcounter != None:
# self.true_pcounter.write(parameter_xxx_dir, plotdir=plotdir + '/true')
if not self.args.no_plot and self.plotdir != '':
self.pcounter.plot(self.plotdir,
subset_by_gene=True,
cyst_positions=self.cyst_positions,
tryp_positions=self.tryp_positions)
if self.true_pcounter != None:
self.true_pcounter.plot(self.plotdir + '/true',
subset_by_gene=True,
cyst_positions=self.cyst_positions,
tryp_positions=self.tryp_positions)
# ----------------------------------------------------------------------------------------
def write_vdjalign_input(self, base_infname):
# first make a list of query names so we can iterate over an ordered collection
ordered_info = []
for query_name in self.input_info:
ordered_info.append(query_name)
queries_per_proc = float(len(self.input_info)) / self.args.n_procs
n_queries_per_proc = int(math.ceil(queries_per_proc))
if self.args.n_procs == 1: # double check for rounding problems or whatnot
assert n_queries_per_proc == len(self.input_info)
for iproc in range(self.args.n_procs):
workdir = self.args.workdir
if self.args.n_procs > 1:
workdir += '/sw-' + str(iproc)
utils.prep_dir(workdir)
infname = workdir + '/' + base_infname
with opener('w')(workdir + '/' + base_infname) as sub_infile:
for iquery in range(iproc * n_queries_per_proc,
(iproc + 1) * n_queries_per_proc):
if iquery >= len(ordered_info):
break
query_name = ordered_info[iquery]
sub_infile.write('>' + str(query_name) + ' NUKES\n')
sub_infile.write(self.input_info[query_name]['seq'] + '\n')
# ----------------------------------------------------------------------------------------
def get_vdjalign_cmd_str(self,
workdir,
base_infname,
base_outfname,
iproc=-1):
"""
Run smith-waterman alignment (from Connor's ighutils package) on the seqs in <base_infname>, and toss all the top matches into <base_outfname>.
"""
# large gap-opening penalty: we want *no* gaps in the middle of the alignments
# match score larger than (negative) mismatch score: we want to *encourage* some level of shm. If they're equal, we tend to end up with short unmutated alignments, which screws everything up
os.environ['PATH'] = os.getenv(
'PWD') + '/packages/samtools:' + os.getenv('PATH')
check_output(['which', 'samtools'])
cmd_str = self.args.ighutil_dir + '/bin/vdjalign align-fastq -q'
if self.args.slurm:
cmd_str = 'srun ' + cmd_str
cmd_str += ' --max-drop 50'
cmd_str += ' --match 5 --mismatch 3'
cmd_str += ' --gap-open 1000'
cmd_str += ' --vdj-dir ' + self.args.datadir
cmd_str += ' ' + workdir + '/' + base_infname + ' ' + workdir + '/' + base_outfname
return cmd_str
# ----------------------------------------------------------------------------------------
def read_output(self, base_outfname, plot_performance=False):
perfplotter = None
if plot_performance:
assert self.args.plotdir != None
assert not self.args.is_data
from performanceplotter import PerformancePlotter
perfplotter = PerformancePlotter(
self.germline_seqs, self.args.plotdir + '/sw/performance',
'sw')
n_processed = 0
for iproc in range(self.args.n_procs):
workdir = self.args.workdir
if self.args.n_procs > 1:
workdir += '/sw-' + str(iproc)
outfname = workdir + '/' + base_outfname
with contextlib.closing(pysam.Samfile(outfname)) as bam:
grouped = itertools.groupby(iter(bam),
operator.attrgetter('qname'))
for _, reads in grouped: # loop over query sequences
self.n_total += 1
self.process_query(bam, list(reads), perfplotter)
n_processed += 1
if not self.args.no_clean:
os.remove(outfname)
if self.args.n_procs > 1: # still need the top-level workdir
os.rmdir(workdir)
print ' processed %d queries' % n_processed
if perfplotter != None:
perfplotter.plot()
# ----------------------------------------------------------------------------------------
def get_choice_prob(self, region, gene):
choice_prob = 1.0
if gene in self.gene_choice_probs[region]:
choice_prob = self.gene_choice_probs[region][gene]
else:
choice_prob = 0.0 # NOTE would it make sense to use something else here?
return choice_prob
# ----------------------------------------------------------------------------------------
def process_query(self, bam, reads, perfplotter=None):
primary = next((r for r in reads if not r.is_secondary), None)
query_seq = primary.seq
try:
query_name = int(
primary.qname
) # if it's just one of my hashes, we want it as an int
except ValueError:
query_name = primary.qname # but if it's someone else's random-ass alphasymbolonumeric string we'll just leave it as-is
raw_best = {}
all_match_names = {}
warnings = {} # ick, this is a messy way to pass stuff around
for region in utils.regions:
all_match_names[region] = []
all_query_bounds, all_germline_bounds = {}, {}
for read in reads: # loop over the matches found for each query sequence
read.seq = query_seq # only the first one has read.seq set by default, so we need to set the rest by hand
gene = bam.references[read.tid]
region = utils.get_region(gene)
warnings[gene] = ''
if region not in raw_best: # best v, d, and j before multiplying by gene choice probs. needed 'cause *these* are the v and j that get excised
raw_best[region] = gene
raw_score = read.tags[0][
1] # raw because they don't include the gene choice probs
score = raw_score
if self.args.apply_choice_probs_in_sw: # NOTE I stopped applying the gene choice probs here because the smith-waterman scores don't correspond to log-probs, so throwing on the gene choice probs was dubious (and didn't seem to work that well)
score = self.get_choice_prob(
region, gene
) * raw_score # multiply by the probability to choose this gene
# set bounds
qrbounds = (read.qstart, read.qend)
glbounds = (read.pos, read.aend)
assert qrbounds[1] - qrbounds[0] == glbounds[1] - glbounds[0]
assert qrbounds[1] <= len(query_seq)
if glbounds[1] > len(self.germline_seqs[region][gene]):
print ' ', gene
print ' ', glbounds[1], len(self.germline_seqs[region][gene])
print ' ', self.germline_seqs[region][gene]
assert glbounds[1] <= len(self.germline_seqs[region][gene])
assert qrbounds[1] - qrbounds[0] == glbounds[1] - glbounds[0]
all_match_names[region].append(
(score, gene)
) # NOTE it is important that this is ordered such that the best match is first
all_query_bounds[gene] = qrbounds
all_germline_bounds[gene] = glbounds
self.summarize_query(query_name, query_seq, raw_best, all_match_names,
all_query_bounds, all_germline_bounds,
perfplotter, warnings)
# ----------------------------------------------------------------------------------------
def print_match(self,
region,
gene,
query_seq,
score,
glbounds,
qrbounds,
codon_pos,
warnings,
skipping=False):
if self.args.debug < 2:
return
out_str_list = []
buff_str = (20 - len(gene)) * ' '
tmp_val = score
if self.args.apply_choice_probs_in_sw and self.get_choice_prob(
region, gene) != 0.0:
tmp_val = score / self.get_choice_prob(region, gene)
if self.args.apply_choice_probs_in_sw:
out_str_list.append(
'%8s%s%s%9.1e * %3.0f = %-6.1f' %
(' ', utils.color_gene(gene), buff_str,
self.get_choice_prob(region, gene), tmp_val, score))
else:
out_str_list.append(
'%8s%s%s%9s%3s %6.0f ' %
(' ', utils.color_gene(gene), '', '', buff_str, score))
out_str_list.append(
'%4d%4d %s\n' %
(glbounds[0], glbounds[1],
self.germline_seqs[region][gene][glbounds[0]:glbounds[1]]))
out_str_list.append('%50s %4d%4d' % ('', qrbounds[0], qrbounds[1]))
out_str_list.append(' %s ' % (utils.color_mutants(
self.germline_seqs[region][gene][glbounds[0]:glbounds[1]],
query_seq[qrbounds[0]:qrbounds[1]])))
if region != 'd':
out_str_list.append(
'(%s %d)' % (utils.conserved_codon_names[region], codon_pos))
if warnings[gene] != '':
out_str_list.append('WARNING ' + warnings[gene])
if skipping:
out_str_list.append('skipping!')
if self.args.outfname == None:
print ''.join(out_str_list)
else:
out_str_list.append('\n')
self.outfile.write(''.join(out_str_list))
# ----------------------------------------------------------------------------------------
def shift_overlapping_boundaries(self, qrbounds, glbounds, query_name,
query_seq, best):
# NOTE this does pretty much the same thing as resolve_overlapping_matches in joinparser.py
""" s-w allows d and j matches (and v and d matches) to overlap... which makes no sense, so apportion the disputed territory between the two regions """
for region_pairs in ({
'left': 'v',
'right': 'd'
}, {
'left': 'd',
'right': 'j'
}):
l_reg = region_pairs['left']
r_reg = region_pairs['right']
l_gene = best[l_reg]
r_gene = best[r_reg]
overlap = qrbounds[l_gene][1] - qrbounds[r_gene][0]
if overlap > 0:
l_length = qrbounds[l_gene][1] - qrbounds[l_gene][0]
r_length = qrbounds[r_gene][1] - qrbounds[r_gene][0]
l_portion, r_portion = 0, 0
while l_portion + r_portion < overlap:
if l_length <= 1 and r_length <= 1: # don't want to erode match (in practice it'll be the d match) all the way to zero
print ' ERROR both lengths went to zero'
assert False
elif l_length > 1 and r_length > 1: # if both have length left, alternate back and forth
if (l_portion + r_portion) % 2 == 0:
l_portion += 1 # give one base to the left
l_length -= 1
else:
r_portion += 1 # and one to the right
r_length -= 1
elif l_length > 1:
l_portion += 1
l_length -= 1
elif r_length > 1:
r_portion += 1
r_length -= 1
if self.args.debug:
print ' WARNING %s apportioning %d bases between %s (%d) match and %s (%d) match' % (
str(query_name), overlap, l_reg, l_portion, r_reg,
r_portion)
assert l_portion + r_portion == overlap
qrbounds[l_gene] = (qrbounds[l_gene][0],
qrbounds[l_gene][1] - l_portion)
glbounds[l_gene] = (glbounds[l_gene][0],
glbounds[l_gene][1] - l_portion)
qrbounds[r_gene] = (qrbounds[r_gene][0] + r_portion,
qrbounds[r_gene][1])
glbounds[r_gene] = (glbounds[r_gene][0] + r_portion,
glbounds[r_gene][1])
best[l_reg + '_gl_seq'] = self.germline_seqs[l_reg][l_gene][
glbounds[l_gene][0]:glbounds[l_gene][1]]
best[l_reg + '_qr_seq'] = query_seq[
qrbounds[l_gene][0]:qrbounds[l_gene][1]]
best[r_reg + '_gl_seq'] = self.germline_seqs[r_reg][r_gene][
glbounds[r_gene][0]:glbounds[r_gene][1]]
best[r_reg + '_qr_seq'] = query_seq[
qrbounds[r_gene][0]:qrbounds[r_gene][1]]
# ----------------------------------------------------------------------------------------
def add_to_info(self,
query_name,
query_seq,
kvals,
match_names,
best,
all_germline_bounds,
all_query_bounds,
codon_positions,
perfplotter=None):
assert query_name not in self.info
self.info[query_name] = {}
self.info[query_name][
'unique_id'] = query_name # redundant, but used somewhere down the line
self.info[query_name]['k_v'] = kvals['v']
self.info[query_name]['k_d'] = kvals['d']
self.info[query_name]['all'] = ':'.join(match_names['v'] +
match_names['d'] +
match_names['j'])
assert codon_positions['v'] != -1
assert codon_positions['j'] != -1
self.info[query_name][
'cdr3_length'] = codon_positions['j'] - codon_positions[
'v'] + 3 #tryp_position_in_joined_seq - self.cyst_position + 3
self.info[query_name]['cyst_position'] = codon_positions['v']
self.info[query_name]['tryp_position'] = codon_positions['j']
# erosion, insertion, mutation info for best match
self.info[query_name]['v_5p_del'] = all_germline_bounds[best['v']][0]
self.info[query_name]['v_3p_del'] = len(
self.germline_seqs['v'][best['v']]) - all_germline_bounds[
best['v']][1] # len(germline v) - gl_match_end
self.info[query_name]['d_5p_del'] = all_germline_bounds[best['d']][0]
self.info[query_name]['d_3p_del'] = len(self.germline_seqs['d'][
best['d']]) - all_germline_bounds[best['d']][1]
self.info[query_name]['j_5p_del'] = all_germline_bounds[best['j']][0]
self.info[query_name]['j_3p_del'] = len(self.germline_seqs['j'][
best['j']]) - all_germline_bounds[best['j']][1]
self.info[query_name][
'fv_insertion'] = query_seq[:all_query_bounds[best['v']][0]]
self.info[query_name]['vd_insertion'] = query_seq[
all_query_bounds[best['v']][1]:all_query_bounds[best['d']][0]]
self.info[query_name]['dj_insertion'] = query_seq[
all_query_bounds[best['d']][1]:all_query_bounds[best['j']][0]]
self.info[query_name]['jf_insertion'] = query_seq[
all_query_bounds[best['j']][1]:]
for region in utils.regions:
self.info[query_name][region + '_gene'] = best[region]
self.info[query_name][region + '_gl_seq'] = best[region +
'_gl_seq']
self.info[query_name][region + '_qr_seq'] = best[region +
'_qr_seq']
self.info['all_best_matches'].add(best[region])
self.info[query_name][
'seq'] = query_seq # only need to add this so I can pass it to print_reco_event
if self.args.debug:
if not self.args.is_data:
utils.print_reco_event(self.germline_seqs,
self.reco_info[query_name],
extra_str=' ',
label='true:')
utils.print_reco_event(self.germline_seqs,
self.info[query_name],
extra_str=' ',
label='inferred:')
if self.pcounter != None:
self.pcounter.increment(self.info[query_name])
if self.true_pcounter != None:
self.true_pcounter.increment(self.reco_info[query_name])
if perfplotter != None:
perfplotter.evaluate(
self.reco_info[query_name],
self.info[query_name]) #, subtract_unphysical_erosions=True)
# ----------------------------------------------------------------------------------------
def summarize_query(self, query_name, query_seq, raw_best, all_match_names,
all_query_bounds, all_germline_bounds, perfplotter,
warnings):
if self.args.debug:
print '%s' % str(query_name)
best, match_names, n_matches = {}, {}, {}
n_used = {'v': 0, 'd': 0, 'j': 0}
k_v_min, k_d_min = 999, 999
k_v_max, k_d_max = 0, 0
for region in utils.regions:
all_match_names[region] = sorted(all_match_names[region],
reverse=True)
match_names[region] = []
codon_positions = {
'v': -1,
'd': -1,
'j': -1
} # conserved codon positions (v:cysteine, d:dummy, j:tryptophan)
for region in utils.regions:
n_matches[region] = len(all_match_names[region])
n_skipped = 0
for score, gene in all_match_names[region]:
glbounds = all_germline_bounds[gene]
qrbounds = all_query_bounds[gene]
assert qrbounds[1] <= len(
query_seq
) # NOTE I'm putting these up avove as well (in process_query), so in time I should remove them from here
assert glbounds[1] <= len(self.germline_seqs[region][gene])
assert qrbounds[0] >= 0
assert glbounds[0] >= 0
glmatchseq = self.germline_seqs[region][gene][
glbounds[0]:glbounds[1]]
# only use the best few matches
if n_used[region] >= int(
self.args.n_max_per_region[utils.regions.index(region)]
): # only take the top few from each region
break
# only use a specified set of genes
if self.args.only_genes != None and gene not in self.args.only_genes:
n_skipped += 1
continue
# add match to the list
n_used[region] += 1
match_names[region].append(gene)
self.print_match(region,
gene,
query_seq,
score,
glbounds,
qrbounds,
-1,
warnings,
skipping=False)
# if the germline match and the query match aren't the same length, s-w likely added an insert, which we shouldn't get since the gap-open penalty is jacked up so high
if len(glmatchseq) != len(
query_seq[qrbounds[0]:qrbounds[1]]
): # neurotic double check (um, I think) EDIT hey this totally saved my ass
print 'ERROR %d not same length' % query_name
print glmatchseq, glbounds[0], glbounds[1]
print query_seq[qrbounds[0]:qrbounds[1]]
assert False
if region == 'v':
this_k_v = all_query_bounds[gene][
1] # NOTE even if the v match doesn't start at the left hand edge of the query sequence, we still measure k_v from there.
# In other words, sw doesn't tell the hmm about it
k_v_min = min(this_k_v, k_v_min)
k_v_max = max(this_k_v, k_v_max)
if region == 'd':
this_k_d = all_query_bounds[gene][1] - all_query_bounds[
raw_best['v']][1] # end of d minus end of v
k_d_min = min(this_k_d, k_d_min)
k_d_max = max(this_k_d, k_d_max)
# check consistency with best match (since the best match is excised in s-w code, and because ham is run with *one* k_v k_d set)
if region not in best:
best[region] = gene
best[region + '_gl_seq'] = self.germline_seqs[region][
gene][glbounds[0]:glbounds[1]]
best[region +
'_qr_seq'] = query_seq[qrbounds[0]:qrbounds[1]]
best[region + '_score'] = score
if self.args.debug and n_skipped > 0:
print '%8s skipped %d %s genes' % ('', n_skipped, region)
for region in utils.regions:
if region not in best:
print ' no', region, 'match found for', query_name # NOTE if no d match found, we should really should just assume entire d was eroded
if not self.args.is_data:
print ' true:'
utils.print_reco_event(self.germline_seqs,
self.reco_info[query_name],
extra_str=' ')
return
# s-w allows d and j matches to overlap... which makes no sense, so arbitrarily give the disputed territory to j
try:
self.shift_overlapping_boundaries(all_query_bounds,
all_germline_bounds, query_name,
query_seq, best)
except AssertionError:
print ' ERROR %s apportionment failed' % str(query_name)
return
for region in utils.regions:
codon_positions[region] = utils.get_conserved_codon_position(
self.cyst_positions, self.tryp_positions, region, best[region],
all_germline_bounds,
all_query_bounds) # position in the query sequence, that is
# check for unproductive rearrangements
try:
# NOTE it's actually expected that this'll fail with a 'sequence too short' error, since the s-w doesn't know it's supposed to make sure the match contains the conserved codons
utils.check_both_conserved_codons(query_seq,
codon_positions['v'],
codon_positions['j'],
debug=self.args.debug,
extra_str=' ')
cdr3_length = codon_positions['j'] - codon_positions['v'] + 3
if cdr3_length % 3 != 0: # make sure we've stayed in frame
if self.args.debug:
print ' out of frame cdr3: %d %% 3 = %d' % (
cdr3_length, cdr3_length % 3)
assert False
utils.check_for_stop_codon(query_seq,
codon_positions['v'],
debug=self.args.debug)
except AssertionError:
if self.args.debug:
print ' unproductive rearrangement in waterer'
if self.args.skip_unproductive:
if self.args.debug:
print ' ...skipping'
self.n_unproductive += 1
self.info['skipped_unproductive_queries'].append(query_name)
return
# best k_v, k_d:
k_v = all_query_bounds[best['v']][1] # end of v match
k_d = all_query_bounds[best['d']][1] - all_query_bounds[best['v']][
1] # end of d minus end of v
if k_d_max < 5: # since the s-w step matches to the longest possible j and then excises it, this sometimes gobbles up the d, resulting in a very short d alignment.
if self.args.debug:
print ' expanding k_d'
k_d_max = max(8, k_d_max)
if 'IGHJ4*' in best['j'] and self.germline_seqs['d'][best['d']][
-5:] == 'ACTAC': # the end of some d versions is the same as the start of some j versions, so the s-w frequently kicks out the 'wrong' alignment
if self.args.debug:
print ' doubly expanding k_d'
if k_d_max - k_d_min < 8:
k_d_min -= 5
k_d_max += 2
k_v_min = max(
0, k_v_min - self.args.default_v_fuzz
) # ok, so I don't *actually* want it to be zero... oh, well
k_v_max += self.args.default_v_fuzz
k_d_min = max(1, k_d_min - self.args.default_d_fuzz)
k_d_max += self.args.default_d_fuzz
assert k_v_min > 0 and k_d_min > 0 and k_v_max > 0 and k_d_max > 0
if self.args.debug:
print ' k_v: %d [%d-%d)' % (k_v, k_v_min, k_v_max)
print ' k_d: %d [%d-%d)' % (k_d, k_d_min, k_d_max)
print ' used',
for region in utils.regions:
print ' %s: %d/%d' % (region, n_used[region],
n_matches[region]),
print ''
kvals = {}
kvals['v'] = {'best': k_v, 'min': k_v_min, 'max': k_v_max}
kvals['d'] = {'best': k_d, 'min': k_d_min, 'max': k_d_max}
self.add_to_info(query_name,
query_seq,
kvals,
match_names,
best,
all_germline_bounds,
all_query_bounds,
codon_positions=codon_positions,
perfplotter=perfplotter)