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Transpose bins 1 and 2 #105

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Transpose bins 1 and 2 #105

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ac50b17
Set bin1 to be tile i-th coord (vertical) and bin2 to be tile j-th (h…
nvictus Sep 17, 2019
05117ad
Remove tile de-mirroring for debugging
nvictus Sep 17, 2019
b05b796
Unpin numpy in travis config
nvictus Sep 17, 2019
d765652
Unpin miniconda installer version in travis to 'latest'
nvictus Sep 17, 2019
549c491
Suppress h5py deprecation warnings
nvictus Sep 17, 2019
fce9636
Fix error of applying dask twice
nvictus Sep 17, 2019
dcda011
Drop weird test
nvictus Sep 17, 2019
1332a75
Maybe fix array_to_hitile
nvictus Sep 17, 2019
bbf27f8
Merge branch 'develop' into transpose-bin-1-2
nvictus Sep 29, 2019
d7da95f
Merge branch 'develop' into transpose-bin-1-2
nvictus Sep 29, 2019
1b2a41a
Add origin identifier to tileset_info
nvictus Sep 30, 2019
b48119b
Change type or mirror_tiles option to bool
nvictus Sep 30, 2019
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74 changes: 33 additions & 41 deletions clodius/tiles/cooler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,8 @@ def get_chromosome_names_cumul_lengths(c):
return chrom_names, chrom_sizes, chrom_cum_lengths


def get_data(f, start_pos_1, end_pos_1, start_pos_2, end_pos_2, transform='default', resolution=None):
def get_data(f, start_pos_1, end_pos_1, start_pos_2, end_pos_2,
transform='default', resolution=None):
"""Get balanced pixel data.

Args:
Expand Down Expand Up @@ -180,7 +181,7 @@ def _get_info_multi_v1(file_path):

c = cooler.Cooler(f["0"])

(chroms, chrom_sizes, chrom_cum_lengths) = get_chromosome_names_cumul_lengths(c)
chroms, chrom_sizes, chrom_cum_lengths = get_chromosome_names_cumul_lengths(c)

total_length = int(chrom_cum_lengths[-1])
max_zoom = f.attrs['max-zoom']
Expand Down Expand Up @@ -228,7 +229,8 @@ def get_quadtree_depth(chromsizes, binsize):


def get_zoom_resolutions(chromsizes, base_res):
return [base_res * 2**x for x in range(get_quadtree_depth(chromsizes, base_res) + 1)]
return [base_res * 2**x
for x in range(get_quadtree_depth(chromsizes, base_res) + 1)]


def print_zoom_resolutions(chromsizes_file, base_res):
Expand All @@ -242,7 +244,8 @@ def print_zoom_resolutions(chromsizes_file, base_res):
print(','.join(str(res) for res in resolutions))


def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos, transform_type='default', x_width=1, y_width=1):
def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos,
transform_type='default', x_width=1, y_width=1):
'''
Generate tiles for a given location. This function retrieves tiles for
a rectangular region of width x_width and height y_width
Expand Down Expand Up @@ -271,19 +274,13 @@ def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos, transform_type='def

tile_size = resolution * BINS_PER_TILE

start1 = x_pos * tile_size
end1 = (x_pos + x_width) * tile_size
start2 = y_pos * tile_size
end2 = (y_pos + y_width) * tile_size

# print("resolution:", resolution)
# print("tile_size:", tile_size)
# print("transform_type:", transform_type);
# print('start1:', start1, end1)
# print('start2:', start2, end2)
start2 = x_pos * tile_size
end2 = (x_pos + x_width) * tile_size
start1 = y_pos * tile_size
end1 = (y_pos + y_width) * tile_size

c = cooler.Cooler(hdf_for_resolution)
(chroms, chrom_sizes, chrom_cum_lengths) = get_chromosome_names_cumul_lengths(c)
chroms, chrom_sizes, chrom_cum_lengths = get_chromosome_names_cumul_lengths(c)

total_length = sum(chrom_sizes.values())

Expand All @@ -292,28 +289,16 @@ def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos, transform_type='def
transform_type, resolution=resolution
)

# print('start1', start1, 'end1', end1, 'weight', len(weight1), 'end1 - start1 / tile_size', (end1 - start1) / resolution)

# print("data:", data)

# print("x_width:", x_width)
# print("y_width:", y_width)
# split out the individual tiles
data_by_tilepos = {}

for x_offset in range(0, x_width):
for y_offset in range(0, y_width):

start1 = (x_pos + x_offset) * tile_size
end1 = (x_pos + x_offset + 1) * tile_size
start2 = (y_pos + y_offset) * tile_size
end2 = (y_pos + y_offset + 1) * tile_size

# print("resolution:", resolution)
# print("tile_size", tile_size)
# print("x_pos:", x_pos, "x_offset", x_offset)
# print("start1", start1, 'end1', end1)
# print("start2", start2, 'end2', end2)
start2 = (x_pos + x_offset) * tile_size
end2 = (x_pos + x_offset + 1) * tile_size
start1 = (y_pos + y_offset) * tile_size
end1 = (y_pos + y_offset + 1) * tile_size

df = data[data['genome_start1'] >= start1]
df = df[df['genome_start1'] < end1]
Expand All @@ -323,8 +308,8 @@ def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos, transform_type='def

binsize = resolution

j = ((df['genome_start1'].values - start1) // binsize).astype(int)
i = ((df['genome_start2'].values - start2) // binsize).astype(int)
i = ((df['genome_start1'].values - start1) // binsize).astype(int)
j = ((df['genome_start2'].values - start2) // binsize).astype(int)

if 'balanced' in df:
v = np.nan_to_num(df['balanced'].values)
Expand Down Expand Up @@ -359,11 +344,11 @@ def make_tiles(hdf_for_resolution, resolution, x_pos, y_pos, transform_type='def
bend1 = bend1[bend1 >= 0]
bend2 = bend2[bend2 >= 0]

out[:, bi] = np.nan
out[bj, :] = np.nan
out[:, bj] = np.nan
out[bi, :] = np.nan

out[:, bend1] = np.nan
out[bend2, :] = np.nan
out[:, bend2] = np.nan
out[bend1, :] = np.nan

# print('sum(isnan1)', isnan1-1)
# print('out.ravel()', sum(np.isnan(out.ravel())), len(out.ravel()))
Expand Down Expand Up @@ -499,7 +484,8 @@ def make_mats(filepath):

c = cooler.Cooler(f['0'])

info['chromsizes'] = [[x[0], int(x[1])] for x in c.chromsizes.iteritems()]
info['chromsizes'] = [[x[0], int(x[1])]
for x in c.chromsizes.iteritems()]
info["min_pos"] = [int(m) for m in info["min_pos"]]
info["max_pos"] = [int(m) for m in info["max_pos"]]
info["max_zoom"] = int(info["max_zoom"])
Expand All @@ -516,6 +502,8 @@ def make_mats(filepath):

mats[filepath] = [f, info]

info['mirror_tiles'] = 'false'
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This is the one line that is neither a coordinate swap nor a whitespace tweak... It is what you intend?

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Nope. I forced no mirroring for debugging purposes. Good catch!

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The problem now is that the client performs "mirroring" by copying lower triangle pixels to the upper triangle, so the result is a white heatmap with pixels painted only on the main diagonal.


return f, info


Expand Down Expand Up @@ -609,9 +597,13 @@ def generate_tiles(filepath, tile_ids):
tileset_file_and_info = mats[filepath]

tile_ids_by_zoom_and_transform = bin_tiles_by_zoom_level_and_transform(
tile_ids).values()
partitioned_tile_ids = list(it.chain(*[hgut.partition_by_adjacent_tiles(t)
for t in tile_ids_by_zoom_and_transform]))
tile_ids
).values()

partitioned_tile_ids = list(
it.chain(*[hgut.partition_by_adjacent_tiles(t)
for t in tile_ids_by_zoom_and_transform])
)

generated_tiles = []

Expand Down