def process_counts(count_file, eq_file, gene_list, allele_idx, allele_lengths,
keep_files):
'''Processes pseudoalignment output, returning compatibility classes.'''
log.info('[alignment] processing pseudoalignment')
# Process count information
counts = dict()
with open(count_file, 'r') as file:
for line in file.read().splitlines():
eq, count = line.split('\t')
counts[eq] = float(count)
# Process compatibility classes
eqs = dict()
with open(eq_file, 'r') as file:
for line in file.read().splitlines():
eq, indices = line.split('\t')
eqs[eq] = indices.split(',')
# Set up compatibility class index
eq_idx = defaultdict(list)
count_unique = 0
count_multi = 0
class_unique = 0
class_multi = 0
for eq, indices in eqs.items():
if [idx for idx in indices if not allele_idx[idx]]:
continue
genes = list({
get_gene(allele)
for idx in indices for allele in allele_idx[idx]
})
count = counts[eq]
if len(genes) == 1 and counts[eq] > 0:
gene = genes[0]
eq_idx[gene].append((indices, count))
count_unique += count
class_unique += 1
else:
count_multi += count
class_multi += 1
# Alleles mapping to their respective compatibility classes
allele_eq = defaultdict(set)
for eqs in eq_idx.values():
for eq, (indices, _) in enumerate(eqs):
for idx in indices:
allele_eq[idx].add(eq)
remove_files([count_file, eq_file], keep_files)
align_stats = [count_unique, count_multi, class_unique, class_multi]
return eq_idx, allele_eq, align_stats
def build_complete(allele):
gene = get_gene(allele)
allele_exons = sorted(exons[allele].items())
coords = [[start,stop] for n,(start,stop) in allele_exons]
seq = [sequences[allele][start:stop] for start,stop in coords]
seq = ''.join(seq)
exon, exon_length = final_exon_length[gene]
if exon in exons[allele]:
start, stop = exons[allele][exon]
if stop-start > exon_length:
seq = seq[:exon_length - (stop - start) + 1]
cDNA[seq].add(allele)
gene_length[gene].append(len(seq))
if allele in utrs:
for (start,stop) in utrs[allele].values():
seq = sequences[allele][start:stop]
other.add(seq)
def process_hla_dat():
'''Processes IMGTHLA database, returning HLA sequences, exon locations,
lists of complete and partial alleles and possible exon combinations.
'''
sequences = dict()
utrs = defaultdict(dict)
exons = defaultdict(dict)
gene_exons = defaultdict(set)
sequence = partial = utr = exon = False
gene_set = set()
complete_alleles = set()
complete_2fields = set()
partial_alleles = set()
with open(hla_dat, 'r') as file:
lines = file.read().splitlines()
for line in lines:
# Denotes end of sequence, add allele to database
if line.startswith('//'):
if sequence and allele in exons:
sequences[allele] = seq
gene_exons[gene].add(number)
gene_set.add(gene)
if not partial:
complete_alleles.add(allele)
complete_2fields.add(process_allele(allele,2))
else:
partial_alleles.add(allele)
partial = False
# Denotes partial alleles
elif line.startswith('FT') and 'partial' in line:
partial = True
# Allele name and gene
elif line.startswith('FT') and re.search('allele\="HLA-', line):
allele = re.split('HLA-', re.sub('["\n]','',line))[1]
gene = get_gene(allele)
exon = sequence = False
seq = ''
# Exon coordinates
elif line.startswith('FT') and re.search('exon',line):
info = re.split('\s+', line)
start = int(info[2].split('..')[0]) - 1
stop = int(info[2].split('..')[1])
exon_coord = [start, stop]
exon = True
# Exon number on following line
elif exon:
number = re.split('"', line)[1]
exons[allele][number] = exon_coord
exon = False
# UTRs
elif line.startswith('FT') and (re.search('\sUTR\s',line)):
info = re.split('\s+', line)
start = int(info[2].split('..')[0]) - 1
stop = int(info[2].split('..')[1])
utr_coord = [start, stop]
if allele not in exons:
utrs[allele]['utr5'] = utr_coord
else:
utrs[allele]['utr3'] = utr_coord
# Start of sequence
elif line.startswith('SQ'):
sequence = True
elif sequence and line.startswith(' '):
seq += ''.join(line.split()[:-1]).upper()
# select only 2-field partial alleles
partial_alleles = {allele for allele in partial_alleles
if process_allele(allele,2) not in complete_2fields}
# get most common final exon length to truncate stop-loss alleles
final_exon_length = defaultdict(list)
for allele in complete_alleles:
gene = get_gene(allele)
exon = sorted(gene_exons[gene])[-1]
if exon not in exons[allele]:
continue
start, stop = exons[allele][exon]
final_exon_length[gene].append(stop-start)
for gene, lengths in final_exon_length.items():
exon = sorted(gene_exons[gene])[-1]
length = get_mode(lengths)
final_exon_length[gene] = [exon,length]
return (complete_alleles, partial_alleles, gene_set, sequences, utrs,
exons, final_exon_length)