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updating for pycirclize version 1.7.1
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FROM python:3.9.17-slim as app | ||
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ARG PYCIRCLIZE_VER="1.7.1" | ||
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# 'LABEL' instructions tag the image with metadata that might be important to the user | ||
LABEL base.image="python:3.9.17-slim" | ||
LABEL dockerfile.version="1" | ||
LABEL software="pyCirclize" | ||
LABEL software.version="${PYCIRCLIZE_VER}" | ||
LABEL description="Circular visualization in Python" | ||
LABEL website="https://github.com/moshi4/pyCirclize" | ||
LABEL license="https://github.com/moshi4/pyCirclize/blob/main/LICENSE" | ||
LABEL maintainer="Erin Young" | ||
LABEL maintainer.email="[email protected]" | ||
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RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
procps && \ | ||
apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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RUN pip install --no-cache pycirclize==${PYCIRCLIZE_VER} -vv | ||
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ENV PATH=$PATH \ | ||
LC_ALL=C | ||
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CMD pip show pycirclize | ||
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WORKDIR /data | ||
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FROM app as test | ||
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WORKDIR /test | ||
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RUN pip show pycirclize | ||
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RUN apt-get update && apt-get install -y --no-install-recommends wget | ||
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RUN wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/pycirclize/1.5.0/tests/example1.py && \ | ||
wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/pycirclize/1.5.0/tests/example2.py && \ | ||
wget -q https://raw.githubusercontent.com/StaPH-B/docker-builds/master/pycirclize/1.5.0/tests/example3.py | ||
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RUN python example1.py && ls example01.png && \ | ||
python example2.py && ls example02.png && \ | ||
python example3.py && ls example03.png |
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# pyCirclize container | ||
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Main tool: [pyCirclize](https://pypi.org/project/pyCirclize/) | ||
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Code repository: https://github.com/moshi4/pyCirclize | ||
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Basic information on how to use this tool: | ||
- executable: NA | ||
- help: NA | ||
- version: NA | ||
- description: pyCirclize is a python package for creating visual images of circular genomes (like those of bacteria) | ||
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Full documentation: https://pypi.org/project/pyCirclize/ | ||
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## Example Usage | ||
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This is for running containers with a specific python package, and is not really meant to be run from the command line. Instead, a bioinformatician could create a python script that uses pycirclize. | ||
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example1.py: | ||
```python | ||
from pycirclize import Circos | ||
import numpy as np | ||
np.random.seed(0) | ||
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# Initialize Circos sectors | ||
sectors = {"A": 10, "B": 15, "C": 12, "D": 20, "E": 15} | ||
circos = Circos(sectors, space=5) | ||
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for sector in circos.sectors: | ||
# Plot sector name | ||
sector.text(f"Sector: {sector.name}", r=110, size=15) | ||
# Create x positions & random y values | ||
x = np.arange(sector.start, sector.end) + 0.5 | ||
y = np.random.randint(0, 100, len(x)) | ||
# Plot lines | ||
track1 = sector.add_track((80, 100), r_pad_ratio=0.1) | ||
track1.xticks_by_interval(interval=1) | ||
track1.axis() | ||
track1.line(x, y) | ||
# Plot points | ||
track2 = sector.add_track((55, 75), r_pad_ratio=0.1) | ||
track2.axis() | ||
track2.scatter(x, y) | ||
# Plot bars | ||
track3 = sector.add_track((30, 50), r_pad_ratio=0.1) | ||
track3.axis() | ||
track3.bar(x, y) | ||
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# Plot links | ||
circos.link(("A", 0, 3), ("B", 15, 12)) | ||
circos.link(("B", 0, 3), ("C", 7, 11), color="skyblue") | ||
circos.link(("C", 2, 5), ("E", 15, 12), color="chocolate", direction=1) | ||
circos.link(("D", 3, 5), ("D", 18, 15), color="lime", ec="black", lw=0.5, hatch="//", direction=2) | ||
circos.link(("D", 8, 10), ("E", 2, 8), color="violet", ec="red", lw=1.0, ls="dashed") | ||
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circos.savefig("example01.png") | ||
``` | ||
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```bash | ||
python example1.py | ||
``` |