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v1.3.0b0
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@shitohana
shitohana committed Nov 2, 2023
1 parent 25d84a5 commit 7f34ab5
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Showing 4 changed files with 49 additions and 22 deletions.
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ build-backend = "hatchling.build"

[project]
name = "bismarkplot"
version = "1.3.0a1"
version = "1.3.0b0"
authors = [
{ name="shitohana", email="kyudytskiy@gmail.com" },
]
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14 changes: 11 additions & 3 deletions src/bismarkplot/BismarkPlot.py
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Expand Up @@ -535,14 +535,16 @@ def from_file(
:param cpu: How many cores to use. Uses every physical core by default
:param batch_size: Number of rows to read by one CPU core
"""
cpu = cpu if cpu is not None else cpu_count()

bismark = pl.read_csv_batched(
file,
separator='\t', has_header=False,
new_columns=['chr', 'position', 'strand',
'count_m', 'count_um', 'context'],
columns=[0, 1, 2, 3, 4, 5],
batch_size=batch_size,
n_threads=cpu if cpu is not None else cpu_count()
n_threads=cpu
)
read_approx = approx_batch_num(file, batch_size)
read_batches = 0
Expand Down Expand Up @@ -722,6 +724,8 @@ def __read_bismark_batches(
batch_size: int = 10 ** 7,
cpu: int = cpu_count()
) -> pl.DataFrame:
cpu = cpu if cpu is not None else cpu_count()

# enable string cache for categorical comparison
pl.enable_string_cache(True)

Expand Down Expand Up @@ -776,7 +780,7 @@ def __read_bismark_batches(
'count_m', 'count_um', 'context'],
columns=[0, 1, 2, 3, 4, 5],
batch_size=batch_size,
n_threads=cpu if cpu is not None else cpu_count()
n_threads=cpu
)
batches = bismark.next_batches(cpu)

Expand Down Expand Up @@ -1469,7 +1473,11 @@ def draw(
else:
subplots_y = 1

subplots_x = (len(self.samples) + len(self.samples) % 2) // subplots_y
if len(self.samples) > 1:
subplots_x = (len(self.samples) + len(self.samples) % 2) // subplots_y
else:
subplots_x = 1

fig, axes = plt.subplots(subplots_y, subplots_x)

if not isinstance(axes, np.ndarray):
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11 changes: 8 additions & 3 deletions src/bismarkplot/console_chrs.py
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Expand Up @@ -10,7 +10,8 @@
)

parser.add_argument('filename', help='path to bismark methylation_extractor file', metavar='path/to/txt')
parser.add_argument('-o', '--out', help='output base name', default=os.path.abspath(os.getcwd()), metavar='DIR')
parser.add_argument('-o', '--out', help='output base name', default="plot", metavar='NAME')
parser.add_argument('-d', '--dir', help='output dir', default=os.path.abspath(os.getcwd()), metavar='DIR')
parser.add_argument('-b', '--batch', help='number of rows to be read from bismark file by batch', type=int, default=10**6, metavar='N')
parser.add_argument('-c', '--cores', help='number of cores to use', type=int, default=None)
parser.add_argument('-w', '--wlength', help='number of windows for chromosome', type=int, default=10**5, metavar='N')
Expand Down Expand Up @@ -42,11 +43,15 @@ def main():
for context in ["CG", "CHG", "CHH"]:
chr.filter(strand=strand, context=context).draw((fig, axes), smooth=args.smooth, label=context)

fig.savefig(f"{args.out}_{strand}.{args.file_format}", dpi=args.dpi)
save_path = f"{args.dir}/{args.out}_{strand}.{args.file_format}"

print(f"Saving to: {save_path}")

fig.savefig(save_path, dpi=args.dpi)

except Exception:
filename = f'error{datetime.now().strftime("%m_%d_%H:%M")}.txt'
file_dir = args.out + '/' + filename
file_dir = args.dir + '/' + filename
with open(file_dir, 'w') as f:
f.write(traceback.format_exc())
print(f'Error happened. Please open an issue at GitHub with Traceback from file: {file_dir}')
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44 changes: 29 additions & 15 deletions src/bismarkplot/console_metagene.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,16 @@
import os
import traceback
from datetime import datetime
from matplotlib.pyplot import close

parser = argparse.ArgumentParser(
prog='BismarkPlot.',
description='Metagene visualizing tool.',
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('filename', help='path to bismark methylation_extractor files', nargs='+')
parser.add_argument('-o', '--out', help='output base name', default=os.path.abspath(os.getcwd()))
parser.add_argument('-o', '--out', help='output base name', default="plot", metavar='NAME')
parser.add_argument('--dir', help='output dir', default=os.path.abspath(os.getcwd()), metavar='DIR')
parser.add_argument('-g', '--genome', help='path to GFF genome file')
parser.add_argument('-r', '--region', help='path to GFF genome file', default="gene", choices=["gene", "exon", "tss", "tes"])
parser.add_argument('-b', '--batch', help='number of rows to be read from bismark file by batch', type=int, default=10**6)
Expand All @@ -28,8 +30,8 @@
parser.add_argument('-S', '--smooth', help='windows for smoothing', type=float, default=10)
parser.add_argument('-L', '--labels', help='labels for plots', nargs='+')
parser.add_argument('-C', '--confidence', help='probability for confidence bands for line-plot. 0 if disabled', type=float, default=0)
parser.add_argument('-H', help='vertical resolution for heat-map', type=int, default=100)
parser.add_argument('-V', help='vertical resolution for heat-map', type=int, default=100)
parser.add_argument('-H', help='vertical resolution for heat-map', type=int, default=100, dest="vresolution")
parser.add_argument('-V', help='vertical resolution for heat-map', type=int, default=100, dest="hresolution")
parser.add_argument("--dpi", help="dpi of output plot", type=int, default=200)

parser.add_argument('-F', '--format', help='format of output plots', choices=['png', 'pdf', 'svg'], default='pdf', dest='file_format')
Expand Down Expand Up @@ -66,26 +68,38 @@ def main():
cpu=args.cores
)

filename = args.dir + "/" + args.out
print(f"Base name for saving: {filename}_<...>.{args.file_format}")

for context in ["CG", "CHG", "CHH"]:
for strand in ["+", "-"]:

filtered = bismark.filter(context=context, strand=strand)
base_name = args.out + "_" + context + strand + "_{type}." + args.file_format
base_name = filename + "_" + context + strand + "_{type}." + args.file_format

if args.line:
fig = filtered.line_plot().draw(smooth=args.smooth, confidence=args.confidence)
fig.savefig(base_name.format(type="line-plot"), dpi = args.dpi)
close()
if args.heatmap:
fig = filtered.heat_map(args.hresolution, args.vresolution).draw()
fig.savefig(base_name.format(type="heat-map"), dpi=args.dpi)
close()
if args.box:
fig = filtered.trim_flank().box_plot()
fig.savefig(base_name.format(type="box-plot"), dpi=args.dpi)
close()
if args.violin:
fig = filtered.trim_flank().violin_plot()
fig.savefig(base_name.format(type="violin-plot"), dpi=args.dpi)
close()

if args.line_plot:
filtered.line_plot().draw(smooth=args.smooth, confidence=args.confidence).savefig(base_name.format(type="line-plot"), dpi = args.dpi)
if args.heat_map:
filtered.heat_map(args.hresolution, args.vresolution).draw().savefig(base_name.format(type="heat-map"), dpi=args.dpi)
if args.box_plot:
filtered.trim_flank().box_plot().savefig(base_name.format(type="box-plot"), dpi=args.dpi)
if args.violin_plot:
filtered.trim_flank().violin_plot().savefig(base_name.format(type="violin-plot"), dpi=args.dpi)

except Exception:
filename = f'error{datetime.now().strftime("%m_%d_%H:%M")}.txt'
with open(args.out + '/' + filename, 'w') as f:
filename = args.dir + '/' + f'error{datetime.now().strftime("%m_%d_%H:%M")}.txt'
with open(filename, 'w') as f:
f.write(traceback.format_exc())
print(f'Error happened. Please open an issue at GitHub with Traceback from file: {f}')
print(f'Error happened. Please open an issue at GitHub with Traceback from file: {filename}')


if __name__ == "__main__":
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