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I've been trying to get pyCirclize to work, but I've run into an error. I feel like I've installed something wrong.
Traceback (most recent call last):
File "/Volumes/IDGenomics_NAS/Bioinformatics/eriny/CirculoCov/moshi_test.py", line 1, in <module>
from pycirclize import Circos
File "/home/eriny/.local/lib/python3.10/site-packages/pycirclize/__init__.py", line 1, in <module>
from pycirclize.circos import Circos
File "/home/eriny/.local/lib/python3.10/site-packages/pycirclize/circos.py", line 24, in <module>
from pycirclize.parser import Bed, Matrix
File "/home/eriny/.local/lib/python3.10/site-packages/pycirclize/parser/__init__.py", line 2, in <module>
from pycirclize.parser.genbank import Genbank
File "/home/eriny/.local/lib/python3.10/site-packages/pycirclize/parser/genbank.py", line 13, in <module>
from Bio.SeqFeature import Seq, SeqFeature, SimpleLocation
ImportError: cannot import name 'SimpleLocation' from 'Bio.SeqFeature' (/home/eriny/.local/lib/python3.10/site-packages/Bio/SeqFeature.py)
I have pyCirclize version 1.2.0, BioPython version 1.79, and am working under python version 3.10.
I installed pyCirclize into my virtual environment with pip install pycirclize --user.
This is the script that I was trying to run (it's from #51).
from pycirclize import Circos
import pandas as pd
import random
random.seed(0)
# Random generate coverage dataframe
chr_size = 6554127
interval = 500
df = pd.DataFrame(
data=[
[1, interval * i + 1, interval * (i + 1), random.randint(50, 200)] for i in range(int(chr_size / interval))
],
columns=["chr", "start", "end", "mean_depth"]
)
print(df)
circos = Circos(sectors={"1": chr_size})
for sector in circos.sectors:
track1 = sector.add_track((65, 70))
track1.axis()
chr_df = df[df["chr"].astype(str) == sector.name]
x = ((chr_df["end"] + chr_df["start"]) / 2).to_numpy()
y = chr_df["mean_depth"].to_numpy()
track2 = sector.add_track((70, 100), r_pad_ratio=0.1)
track2.fill_between(x, y, color="skyblue")
circos.savefig("example.png")
The text was updated successfully, but these errors were encountered:
I've been trying to get pyCirclize to work, but I've run into an error. I feel like I've installed something wrong.
I have pyCirclize version 1.2.0, BioPython version 1.79, and am working under python version 3.10.
I installed pyCirclize into my virtual environment with
pip install pycirclize --user
.This is the script that I was trying to run (it's from #51).
The text was updated successfully, but these errors were encountered: