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Fix array length when chr length < window (thanks @lkulandaivelu, #686)
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@tanghaibao
tanghaibao committed Jul 10, 2024
1 parent daf23d8 commit 4754dc9
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5 changes: 5 additions & 0 deletions jcvi/graphics/landscape.py
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Expand Up @@ -1062,6 +1062,10 @@ def stackarray(binfile: BinFile, chr: str, window: int, shift: int):
n = np.array(n, dtype=float)

w = window // shift
nw = m.shape[0]
if nw < w:
logger.info("%s length < window, using %d bins instead of %d", chr, nw, w)
w = nw
m = moving_sum(m, window=w)
n = moving_sum(n, window=w)
m /= n
Expand Down Expand Up @@ -1215,6 +1219,7 @@ def stack(args):
pf = fastafile.rsplit(".", 1)[0]
image_name = pf + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
return image_name


if __name__ == "__main__":
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Binary file added tests/graphics/data/TAIR10_organelles.fas.gz
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321 changes: 321 additions & 0 deletions tests/graphics/data/exons.bed
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16 changes: 16 additions & 0 deletions tests/graphics/test_landscape.py
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import os
import os.path as op

from jcvi.apps.base import cleanup
from jcvi.graphics.landscape import stack


def test_stack():
cwd = os.getcwd()
os.chdir(op.join(op.dirname(__file__), "data"))
cleanup("TAIR10_organelles.fas.pdf")
image_name = stack(
["TAIR10_organelles.fas.gz", "--stacks=exons", "--window=25000", "--shift=5000"]
)
assert op.exists(image_name)
os.chdir(cwd)

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