def get_num_unassigned(simulation_output_dir):
fq_fname = '%s/reads_split/cell_unassigned_barcodes.fastq.gz' % \
(simulation_output_dir)
num_unassigned = 0
fq_file = gzip.open(fq_fname, 'rb')
fq_iter = IO_utils.read_fastq_sequential(fq_file)
for (lines, _) in fq_iter:
num_unassigned += 1
return num_unassigned
def get_fraction_consistent(pred_bc, simulation_output_dir):
fq_fname = '%s/reads_split/cell_%s_barcodes.fastq.gz' % \
(simulation_output_dir, pred_bc)
if not os.path.exists(fq_fname):
return 0
fq_file = gzip.open(fq_fname, 'rb')
fq_iter = IO_utils.read_fastq_sequential(fq_file)
assignments = Counter()
total_reads = 0
for (lines, _) in fq_iter:
read_name = lines[0]
assigned_bc = read_name.split(':')[-2].split('_')[0]
assignments.update([assigned_bc])
total_reads += 1
try:
common_bc, count = assignments.most_common()[0]
return count / total_reads
except IndexError:
return 0
def get_fraction_correct_reads(pred_bc, simulation_output_dir):
fq_fname = '%s/reads_split/cell_%s_barcodes.fastq.gz' % \
(simulation_output_dir, pred_bc)
if not os.path.exists(fq_fname):
return (0, 0)
fq_file = gzip.open(fq_fname, 'rb')
fq_iter = IO_utils.read_fastq_sequential(fq_file)
tpr = 0.
fpr = 0.
for (lines, _) in fq_iter:
read_name = lines[0]
assigned_bc = read_name.split(':')[-1]
true_bc = read_name.split(':')[-2].split('_')[0]
if (assigned_bc == true_bc):
tpr += 1.
else:
fpr += 1.
total_reads = tpr + fpr
tpr /= total_reads
fpr /= total_reads
return (tpr, fpr)
