bio2zarr 0.0.2__tar.gz

bio2zarr-0.0.2/.gitignore

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+# Byte-compiled / optimized / DLL files
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bio2zarr-0.0.2/CHANGELOG.md

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+# 0.0.2 2024-03-27
+
+- Merged 1D and 2D encode steps into one, and change rate reporting to bytes
+- Add --max-memory for encode
+- Change `chunk_width` to `samples_chunk_size` and `chunk_length` to `variants_chunk_size`
+- Various updates to the intermediate chunked format, with breaking change to version 0.2
+- Add distributed explode commands

bio2zarr-0.0.2/LICENSE

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bio2zarr-0.0.2/MANIFEST.in

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+prune tests

bio2zarr-0.0.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: bio2zarr
+Version: 0.0.2
+Summary: Convert bioinformatics data to Zarr
+Home-page: https://github.com/pystatgen/bio2zarr
+Author: sgkit Developers
+Author-email: project@pystatgen.org
+License: Apache
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: zarr!=2.11.0,!=2.11.1,!=2.11.2,>=2.10.0
+Requires-Dist: click
+Requires-Dist: tabulate
+Requires-Dist: tqdm
+Requires-Dist: humanfriendly
+Requires-Dist: cyvcf2
+Requires-Dist: bed_reader
+
+
+This is an early alpha release for testing and development.
+**Do not use in production**

bio2zarr-0.0.2/README.md

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+# bio2zarr
+Convert bioinformatics file formats to Zarr
+
+Initially supports converting VCF to the
+[sgkit vcf-zarr specification](https://github.com/pystatgen/vcf-zarr-spec/)
+
+**This is early alpha-status code: everything is subject to change,
+and it has not been thoroughly tested**
+
+## Install
+
+```
+$ python3 -m pip install bio2zarr
+```
+
+This will install the programs ``vcf2zarr``, ``plink2zarr`` and ``vcf_partition``
+into your local Python path. You may need to update your $PATH to call the 
+executables directly.
+
+Alternatively, calling 
+```
+$ python3 -m bio2zarr vcf2zarr <args>
+```
+is equivalent to 
+
+```
+$ vcf2zarr <args>
+```
+and will always work.
+
+
+## vcf2zarr
+
+Convert a VCF to zarr format:
+
+```
+$ vcf2zarr convert <VCF1> <VCF2> <zarr>
+```
+
+Converts the VCF to zarr format.
+
+**Do not use this for anything but the smallest files**
+
+The recommended approach is to use a multi-stage conversion
+
+First, convert the VCF into the intermediate format:
+
+```
+vcf2zarr explode tests/data/vcf/sample.vcf.gz tmp/sample.exploded
+```
+
+Then, (optionally) inspect this representation to get a feel for your dataset
+```
+vcf2zarr inspect tmp/sample.exploded
+```
+
+Then, (optionally) generate a conversion schema to describe the corresponding
+Zarr arrays:
+
+```
+vcf2zarr mkschema tmp/sample.exploded > sample.schema.json
+```
+
+View and edit the schema, deleting any columns you don't want, or tweaking 
+dtypes and compression settings to your taste.
+
+Finally, encode to Zarr:
+```
+vcf2zarr encode tmp/sample.exploded tmp/sample.zarr -s sample.schema.json
+```
+
+Use the ``-p, --worker-processes`` argument to control the number of workers used
+in the ``explode`` and ``encode`` phases.
+
+## plink2zarr
+
+Convert a plink ``.bed`` file to zarr format. **This is incomplete**
+
+## vcf_partition
+
+Partition a given VCF file into (approximately) a give number of regions:
+
+```
+vcf_partition 20201028_CCDG_14151_B01_GRM_WGS_2020-08-05_chr20.recalibrated_variants.vcf.gz -n 10
+```
+gives
+```
+chr20:1-6799360
+chr20:6799361-14319616
+chr20:14319617-21790720
+chr20:21790721-28770304
+chr20:28770305-31096832
+chr20:31096833-38043648
+chr20:38043649-45580288
+chr20:45580289-52117504
+chr20:52117505-58834944
+chr20:58834945-
+```
+
+These reqion strings can then be used to split computation of the VCF 
+into chunks for parallelisation.
+
+**TODO give a nice example here using xargs**
+
+**WARNING that this does not take into account that indels may overlap 
+partitions and you may count variants twice or more if they do**

bio2zarr-0.0.2/bio2zarr/__init__.py

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+from . provenance import __version__

bio2zarr-0.0.2/bio2zarr/__main__.py

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+import click
+
+from . import cli
+
+@cli.version
+@click.group()
+def bio2zarr():
+    pass
+
+# Provide a single top-level interface to all of the functionality.
+# This probably isn't the recommended way of interacting, as we
+# install individual commands as console scripts. However, this
+# is handy for development and for those whose PATHs aren't set
+# up in the right way.
+bio2zarr.add_command(cli.vcf2zarr)
+bio2zarr.add_command(cli.plink2zarr)
+bio2zarr.add_command(cli.vcf_partition)
+
+if __name__ == "__main__":
+    bio2zarr()

bio2zarr-0.0.2/bio2zarr/_version.py

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+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.0.2'
+__version_tuple__ = version_tuple = (0, 0, 2)