Split from https://github.com/JannesSP/read5

CITATION.cff

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+cff-version: 1.2.1
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Spangenberg"
+    given-names: "Jannes"
+    orcid: "https://orcid.org/0000-0002-6126-411X"
+title: "Read5"
+version: 1.2.1
+date-released: 2023-07-11

MANIFEST.in

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+include versioneer.py
+graft tests

README.md

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+# ![Alt text](figures/logo.png)
+
+- **Read5** is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs. ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/read5)
+- **Read5_ont** is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs. ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/read5_ont)
+
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-teal.svg)](https://www.gnu.org/licenses/gpl-3.0)
+
+[![PyPI](https://img.shields.io/pypi/v/read5) ![PyPI - Downloads](https://img.shields.io/pypi/dm/read5) ![PyPI - Status](https://img.shields.io/pypi/status/read5)](https://pypi.org/project/read5/)
+
+
+[![Anaconda-Server Badge](https://anaconda.org/jannessp/read5/badges/version.svg)](https://anaconda.org/jannessp/read5) ![Conda](https://img.shields.io/conda/dn/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/latest_release_date.svg)](https://anaconda.org/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/platforms.svg)](https://anaconda.org/jannessp/read5)
+
+[![DOI](https://zenodo.org/badge/633012569.svg)](https://zenodo.org/badge/latestdoi/633012569)
+
+[![Twitter Follow](https://img.shields.io/twitter/follow/Ja_Spangenberg)](https://twitter.com/Ja_Spangenberg)
+___
+## Table of Content
+1.  [Installation](#installation)
+2.  [Usage](#usage)
+3.  [Full Documentation](https://jannessp.github.io/read5.github.io/)
+___
+## Installation
+
+### Pypi/pip
+```bash
+pip install read5
+# or
+pip install read5_ont
+```
+### Conda
+Pod5 is now available via [conda](https://anaconda.org/jannessp/pod5) (19.07.2023).
+
+```bash
+conda install mamba
+mamba create -n read5 -c jannessp read5
+conda activate read5
+# or
+mamba create -n read5_ont -c jannessp read5_ont
+conda activate read5_ont
+```
+Alternatively you can create the environment using the [conda.recipe/env.yml](conda.recipe/env.yml) file.
+```bash
+conda install mamba
+mamba env create -f conda.recipe/env.yml
+conda activate read5
+```
+___
+## Usage
+
+[Click here to see a full documentation about the classes and function.](https://jannessp.github.io/read5.github.io/)
+
+*my_file* can be a fast5, slow5, blow5 or pod5 file. The wrapper detects the file format depending on the file extension.
+
+### Small example:
+
+```python
+from read5 import read # or from read5.Reader import read
+
+r5 = read(my_file) # file with on of these extensions: .fast5, .slow5, .blow5, .pod5
+for readid in r5:
+    signal = r5.getSignal(readid) # returns raw integer values stored in the file
+    pA_signal = r5.getpASignal(readid) # returns pA signal
+    norm_signal = r5.getZNormSignal(readid) # returns normalised read signal: norm_signal = (signal - median(signal)) / mad(signal)
+    channel = r5.getChannelNumber(readid)
+    sampleid = r5.getSampleID(readid)
+    runid = r5.getRunID(readid)
+
+readid_list = r5.getReads()
+```
+
+### File Reader Classes
+If you want to use the file readers you can import the corresponding class like this:
+
+```python
+from read5.Fast5Reader import Fast5Reader # contains the Fast5 Reader class
+from read5.Slow5Reader import Slow5Reader # contains the Slow5 Reader class - !not available in read5_ont!
+from read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class
+```
+
+### Abstract File Reader Class
+
+```python
+from read5.AbstractFileReader import AbstractFileReader
+```
+
+### Possible Exceptions
+
+```python
+from read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode
+```
+
+- UnknownFileFormatException: is raised, when the file extension does not match one of ['.fast5', '.slow5', '.blow5', '.pod5'] (or ['.fast5', '.pod5'] in **read5_ont**)
+- UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function
+
+## Full Documentation
+Created with [pdoc3](https://pdoc3.github.io/pdoc/).
+Can be found [here](https://jannessp.github.io/read5.github.io/).

README.rst

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+Installation
+------------
+
+Pypi/pip
+~~~~~~~~
+
+.. code:: bash
+
+   pip install read5_ont
+
+Conda
+~~~~~
+
+Pod5 is now available via `conda <https://anaconda.org/jannessp/pod5>`__ (19.07.2023).
+
+.. code:: bash
+
+   conda install mamba
+   mamba create -n read5_ont -c jannessp read5_ont
+   conda activate read5_ont
+
+Alternatively you can create the environment using the
+`conda.recipe/env.yml <conda.recipe/env.yml>`__ file.
+
+.. code:: bash
+
+   conda install mamba
+   mamba env create -f conda.recipe/env.yml
+   conda activate read5_ont
+
+--------------
+
+Usage
+-----
+
+`Click here to see a full documentation about the classes and
+function. <https://jannessp.github.io/read5.github.io/>`__
+
+*my_file* can be a fast5 or pod5 file. The wrapper detects
+the file format depending on the file extension.
+
+Small example:
+~~~~~~~~~~~~~~
+
+.. code:: python
+
+   from read5 import read # or from read5.Reader import read
+
+   r5 = read(my_file) # file with on of these extensions: .fast5, .pod5
+   for readid in r5:
+       signal = r5.getSignal(readid) # returns raw integer values stored in the file
+       pA_signal = r5.getpASignal(readid) # returns pA signal
+       norm_signal = r5.getZNormSignal(readid) # returns normalised read signal: norm_signal = (signal - median(signal)) / mad(signal)
+       channel = r5.getChannelNumber(readid)
+       sampleid = r5.getSampleID(readid)
+       runid = r5.getRunID(readid)
+
+   readid_list = r5.getReads()
+
+File Reader Classes
+~~~~~~~~~~~~~~~~~~~
+
+If you want to use the file readers you can import the corresponding
+class like this:
+
+.. code:: python
+
+   from read5.Fast5Reader import Fast5Reader # contains the Fast5 Reader class
+   from read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class
+
+Abstract File Reader Class
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. code:: python
+
+   from read5.AbstractFileReader import AbstractFileReader
+
+Possible Exceptions
+~~~~~~~~~~~~~~~~~~~
+
+.. code:: python
+
+   from read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode
+
+-  UnknownFileFormatException: is raised, when the file extension does
+   not match one of [‘.fast5’, ‘.pod5’]
+-  UnknownNormalizationMode: is raised, when an unknown mode is provided
+   for the signal normalization function
+
+Full Documentation
+------------------
+
+Created with `pdoc3 <https://pdoc3.github.io/pdoc/>`__. Can be found
+`here <https://jannessp.github.io/read5.github.io/>`__.

conda.recipe/README.md

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+# Run
+```bash
+conda mambabuild conda.recipe/
+conda convert --platform osx-64 /path/to/package.tar.bz2 -o outputdir/
+```

conda.recipe/conda_build_config.yaml

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+python:
+  - 3.8
+  - 3.9
+  - 3.10
+  - 3.11 # not with pyslow5 (has no 3.11 package)
+# - 3.12 # not with pod5 (has no 3.12 package)

conda.recipe/env.yml

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+name: read5
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+  - jannessp
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - aws-c-auth=0.7.0=hf8751d9_2
+  - aws-c-cal=0.6.0=h93469e0_0
+  - aws-c-common=0.8.23=hd590300_0
+  - aws-c-compression=0.2.17=h862ab75_1
+  - aws-c-event-stream=0.3.1=h9599702_1
+  - aws-c-http=0.7.11=hbe98c3e_0
+  - aws-c-io=0.13.28=h3870b5a_0
+  - aws-c-mqtt=0.8.14=h2e270ba_2
+  - aws-c-s3=0.3.13=heb0bb06_2
+  - aws-c-sdkutils=0.1.11=h862ab75_1
+  - aws-checksums=0.1.16=h862ab75_1
+  - aws-crt-cpp=0.20.3=he9c0e7f_4
+  - aws-sdk-cpp=1.10.57=hbc2ea52_17
+  - boltons=23.0.0=pyhd8ed1ab_0
+  - brotli=1.0.9=h166bdaf_9
+  - brotli-bin=1.0.9=h166bdaf_9
+  - brotli-python=1.0.9=py310hd8f1fbe_9
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.19.1=hd590300_0
+  - ca-certificates=2023.5.7=hbcca054_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - certifi=2023.5.7=pyhd8ed1ab_0
+  - cffi=1.15.1=py310h255011f_3
+  - charset-normalizer=3.1.0=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - conda=23.5.0=py310hff52083_1
+  - conda-package-handling=2.0.2=pyh38be061_0
+  - conda-package-streaming=0.8.0=pyhd8ed1ab_0
+  - cryptography=41.0.1=py310h75e40e8_0
+  - exceptiongroup=1.1.1=pyhd8ed1ab_0
+  - fmt=9.1.0=h924138e_0
+  - gflags=2.2.2=he1b5a44_1004
+  - glog=0.6.0=h6f12383_0
+  - h5py=3.8.0=nompi_py310h0311031_100
+  - hdf5=1.12.2=nompi_h4df4325_101
+  - icu=72.1=hcb278e6_0
+  - idna=3.4=pyhd8ed1ab_0
+  - importlib-metadata=6.7.0=pyha770c72_0
+  - iniconfig=2.0.0=pyhd8ed1ab_0
+  - iso8601=2.0.0=pyhd8ed1ab_0
+  - jsonpatch=1.32=pyhd8ed1ab_0
+  - jsonpointer=2.0=py_0
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.20.1=h81ceb04_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lib-pod5=0.2.4=py310_0
+  - libabseil=20230125.3=cxx17_h59595ed_0
+  - libaec=1.0.6=hcb278e6_1
+  - libarchive=3.6.2=h039dbb9_1
+  - libarrow=11.0.0=h657c46f_30_cpu
+  - libblas=3.9.0=17_linux64_openblas
+  - libbrotlicommon=1.0.9=h166bdaf_9
+  - libbrotlidec=1.0.9=h166bdaf_9
+  - libbrotlienc=1.0.9=h166bdaf_9
+  - libcblas=3.9.0=17_linux64_openblas
+  - libcrc32c=1.1.2=h9c3ff4c_0
+  - libcurl=8.1.2=h409715c_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libevent=2.1.12=hf998b51_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=13.1.0=he5830b7_0
+  - libgfortran-ng=13.1.0=h69a702a_0
+  - libgfortran5=13.1.0=h15d22d2_0
+  - libgomp=13.1.0=he5830b7_0
+  - libgoogle-cloud=2.12.0=h840a212_1
+  - libgrpc=1.56.2=h3905398_0
+  - libiconv=1.17=h166bdaf_0
+  - liblapack=3.9.0=17_linux64_openblas
+  - libmamba=1.4.5=h658169a_0
+  - libmambapy=1.4.5=py310h8aae740_0
+  - libnghttp2=1.52.0=h61bc06f_0
+  - libnsl=2.0.0=h7f98852_0
+  - libnuma=2.0.16=h0b41bf4_1
+  - libopenblas=0.3.23=pthreads_h80387f5_0
+  - libprotobuf=4.23.3=hd1fb520_0
+  - libsolv=0.7.24=hfc55251_1
+  - libsqlite=3.42.0=h2797004_0
+  - libssh2=1.11.0=h0841786_0
+  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libthrift=0.18.1=h8fd135c_2
+  - libutf8proc=2.8.0=h166bdaf_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libxml2=2.11.4=h0d562d8_0
+  - libzlib=1.2.13=hd590300_5
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - mako=1.2.4=pyhd8ed1ab_0
+  - mamba=1.4.5=py310h51d5547_0
+  - markdown=3.4.3=pyhd8ed1ab_0
+  - markupsafe=2.1.3=py310h2372a71_0
+  - more-itertools=9.1.0=pyhd8ed1ab_0
+  - ncurses=6.4=hcb278e6_0
+  - numpy=1.25.0=py310ha4c1d20_0
+  - ont_vbz_hdf_plugin=1.0.1=h3f9cce5_5
+  - openssl=3.1.1=hd590300_1
+  - orc=1.9.0=h385abfd_1
+  - packaging=23.1=pyhd8ed1ab_0
+  - pdoc3=0.8.1=py_0
+  - pip=23.2=pyhd8ed1ab_0
+  - pluggy=1.2.0=pyhd8ed1ab_0
+  - pod5=0.2.4=py310_0
+  - polars=0.17.14=py310hcb5633a_0
+  - pyarrow=11.0.0=py310he6bfd7f_30_cpu
+  - pybind11-abi=4=hd8ed1ab_3
+  - pycosat=0.6.4=py310h5764c6d_1
+  - pycparser=2.21=pyhd8ed1ab_0
+  - pyopenssl=23.2.0=pyhd8ed1ab_1
+  - pyslow5=1.0.0=py310h1ae98be_3
+  - pysocks=1.7.1=pyha2e5f31_6
+  - pytest=7.4.0=pyhd8ed1ab_0
+  - python=3.10.12=hd12c33a_0_cpython
+  - python_abi=3.10=3_cp310
+  - pytz=2023.3=pyhd8ed1ab_0
+  - rdma-core=28.9=h59595ed_1
+  - re2=2023.03.02=h8c504da_0
+  - readline=8.2=h8228510_1
+  - reproc=14.2.4=h0b41bf4_0
+  - reproc-cpp=14.2.4=hcb278e6_0
+  - requests=2.31.0=pyhd8ed1ab_0
+  - ruamel.yaml=0.17.32=py310h2372a71_0
+  - ruamel.yaml.clib=0.2.7=py310h1fa729e_1
+  - s2n=1.3.46=h06160fa_0
+  - setuptools=68.0.0=pyhd8ed1ab_0
+  - snappy=1.1.10=h9fff704_0
+  - tk=8.6.12=h27826a3_0
+  - tomli=2.0.1=pyhd8ed1ab_0
+  - toolz=0.12.0=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - typing_extensions=4.7.1=pyha770c72_0
+  - tzdata=2023c=h71feb2d_0
+  - ucx=1.14.1=hf587318_2
+  - urllib3=2.0.3=pyhd8ed1ab_1
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - xz=5.2.6=h166bdaf_0
+  - yaml-cpp=0.7.0=h27087fc_2
+  - zipp=3.15.0=pyhd8ed1ab_0
+  - zlib=1.2.13=hd590300_5
+  - zstandard=0.19.0=py310h1275a96_2
+  - zstd=1.5.2=h3eb15da_6