def get_barcode_windows_seperate(fragments, barcode_map, window_size,
chrom_length, start, end, walk_step):
window_starts = range(start, end - 2 * window_size, walk_step)
barcode_windows = []
for start in window_starts:
#up windows
end = start + window_size
overlap = utilities.frags_overlap_same_chrom(fragments, start, end)
barcodes = set(barcode_map[bc] for bc in overlap["bc"])
barcode_windows.append(barcodes)
barcode_windows.append(set([start, end]))
#down windows, need to change the start by start + windows size
start1 = start + window_size + 1
end1 = start1 + window_size
overlap1 = utilities.frags_overlap_same_chrom(fragments, start1, end1)
barcodes1 = set(barcode_map[bc1] for bc1 in overlap1["bc"])
barcode_windows.append(barcodes1)
barcode_windows.append(set([start1, end1]))
return barcode_windows
def get_barcode_windows(fragments, barcode_map, window_size, chrom_length,
start, end):
window_starts = range(start, end, window_size)
barcode_windows = []
for start in window_starts:
end = start + window_size
overlap = utilities.frags_overlap_same_chrom(fragments, start, end)
barcodes = set(barcode_map[bc] for bc in overlap["bc"])
barcode_windows.append(barcodes)
return barcode_windows
def get_bg_fragments_distributions(frags, reference, logger, skip_length=1e6):
distributions = []
for chrom in reference.chroms:
logger.log("BG Frag Length Distribution: {}".format(chrom))
chrom_length = reference.chrom_lengths[chrom]
curfrags = frags.loc[frags["chrom"] == chrom]
if chrom_length < 2 * skip_length: continue
for pos in numpy.arange(skip_length, chrom_length - skip_length,
skip_length):
e = utilities.frags_overlap_same_chrom(curfrags, int(pos),
int(pos))
if e.shape[0] < 5:
continue
distributions.append(e["obs_len"].values)
if len(distributions) < 2 and skip_length > 1e5:
print("Trying again...")
return get_bg_fragments_distributions(frags,
reference,
logger,
skip_length=5e4)
return distributions