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updating for pycirclize version 1.7.1 (#1066)
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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 | ||
| ``` |