def _consumer(input_queue, output_queue):
while True:
line = input_queue.get()
if line is None:
break
f = BEDFeature.from_string(line)
# retrieve conservation data
bigwig_file = chrom_bigwig_dict[f.chrom]
arr = extract_bigwig_data(f, bigwig_file)
# measure conservation at various sliding windows
window_scores = []
for window_size in window_sizes:
window_scores.append(best_sliding_window(arr, window_size, np.mean))
# measure average conservation
finitearr = arr[np.isfinite(arr)]
if len(finitearr) == 0:
mean_cons = np.nan
else:
mean_cons = np.mean(finitearr)
fields = [f.name, '%s:%d-%d[%s]' % (f.chrom, f.tx_start, f.tx_end, f.strand),
str(len(arr)), str(mean_cons)]
fields.extend(map(str,window_scores))
result = '\t'.join(fields)
output_queue.put(result)
output_queue.put(None)
def _consumer(input_queue, output_queue):
while True:
line = input_queue.get()
if line is None:
break
f = BEDFeature.from_string(line)
# retrieve conservation data
bigwig_file = chrom_bigwig_dict[f.chrom]
arr = extract_bigwig_data(f, bigwig_file)
# measure conservation at various sliding windows
window_scores = []
for window_size in window_sizes:
window_scores.append(
best_sliding_window(arr, window_size, np.mean))
# measure average conservation
finitearr = arr[np.isfinite(arr)]
if len(finitearr) == 0:
mean_cons = np.nan
else:
mean_cons = np.mean(finitearr)
fields = [
f.name,
'%s:%d-%d[%s]' % (f.chrom, f.tx_start, f.tx_end, f.strand),
str(len(arr)),
str(mean_cons)
]
fields.extend(map(str, window_scores))
result = '\t'.join(fields)
output_queue.put(result)
output_queue.put(None)
def _consumer(input_queue, output_queue):
while True:
line = input_queue.get()
if line is None:
break
f = BEDFeature.from_string(line)
fields = feature_conservation(f, chrom_bigwig_dict, sig_threshold,
window_sizes)
output_queue.put('\t'.join(fields))
output_queue.put(None)
def _consumer(input_queue, output_queue):
while True:
line = input_queue.get()
if line is None:
break
f = BEDFeature.from_string(line)
fields = feature_conservation(f, chrom_bigwig_dict,
sig_threshold, window_sizes)
output_queue.put('\t'.join(fields))
output_queue.put(None)
