bio2zarr 0.0.6__tar.gz → 0.0.9__tar.gz

bio2zarr-0.0.9/.github/workflows/ci.yml

@@ -0,0 +1,34 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+
+jobs:
+  pre-commit:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - uses: pre-commit/action@v3.0.1
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+      - run: pytest

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/.gitignore

@@ -1,3 +1,6 @@
+# auto generated by setuptools_scm and configured in pyproject.toml
+bio2zarr/_version.py
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -152,9 +155,9 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
-# PyCharm
-#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
-#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
-#  and can be added to the global gitignore or merged into this file.  For a more nuclear
-#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+# IDE
+.vscode
+.idea
+
+# Mac
+.DS_Store

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/.pre-commit-config.yaml

@@ -8,7 +8,7 @@ repos:
       - id: check-case-conflict
       - id: check-yaml
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+    rev: v0.4.2
     hooks:
       - id: ruff
         args: [ --fix ]

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/CHANGELOG.md

@@ -1,3 +1,15 @@
+# 0.0.9 2024-05-02
+
+- Change on-disk format for explode and schema
+- Support older tabix indexes
+- Fix some bugs in explode
+
+# 0.0.8 2024-04-30
+
+- Change on-disk format of distributed encode and simplify
+- Check for all partitions nominally completed encoding before doing
+  anything destructive in dencode-finalise
+
 # 0.0.6 2024-04-24
 
 - Only use NOSHUFFLE by default on ``call_genotype`` and bool arrays.

bio2zarr-0.0.9/PKG-INFO

@@ -0,0 +1,363 @@
+Metadata-Version: 2.1
+Name: bio2zarr
+Version: 0.0.9
+Summary: Convert bioinformatics data to Zarr
+Author-email: sgkit Developers <project@sgkit.dev>
+License:                                  Apache License
+                                   Version 2.0, January 2004
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+        
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+Project-URL: repository, https://github.com/sgkit-dev/bio2zarr
+Project-URL: documentation, https://sgkit-dev.github.io/bio2zarr/intro.html
+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/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: zarr>=2.17
+Requires-Dist: click
+Requires-Dist: tabulate
+Requires-Dist: tqdm
+Requires-Dist: humanfriendly
+Requires-Dist: cyvcf2
+Requires-Dist: bed_reader
+Provides-Extra: dev
+Requires-Dist: msprime; extra == "dev"
+Requires-Dist: pysam; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-coverage; extra == "dev"
+Requires-Dist: pytest-xdist; extra == "dev"
+Requires-Dist: sgkit>=0.8.0; extra == "dev"
+Requires-Dist: tqdm; extra == "dev"
+
+[![CI](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml)
+
+# 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.
+
+### Shell completion
+
+To enable shell completion for a particular session in Bash do:
+
+```
+eval "$(_VCF2ZARR_COMPLETE=bash_source vcf2zarr)" 
+```
+
+If you add this to your ``.bashrc`` vcf2zarr shell completion should available
+in all new shell sessions.
+
+See the [Click documentation](https://click.palletsprojects.com/en/8.1.x/shell-completion/#enabling-completion)
+for instructions on how to enable completion in other shells.
+a
+
+## 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-0.0.6 → bio2zarr-0.0.9}/README.md

@@ -1,3 +1,5 @@
+[![CI](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/sgkit-dev/bio2zarr/actions/workflows/ci.yml)
+
 # bio2zarr
 Convert bioinformatics file formats to Zarr
 

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/bio2zarr/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6'
-__version_tuple__ = version_tuple = (0, 0, 6)
+__version__ = version = '0.0.9'
+__version_tuple__ = version_tuple = (0, 0, 9)

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/bio2zarr/cli.py

@@ -233,7 +233,7 @@ def dexplode_partition(icf_path, partition, verbose):
     from 0 (inclusive) to the number of paritions returned by dexplode_init (exclusive).
     """
     setup_logging(verbose)
-    vcf.explode_partition(icf_path, partition, show_progress=False)
+    vcf.explode_partition(icf_path, partition)
 
 
 @click.command

{bio2zarr-0.0.6 → bio2zarr-0.0.9}/bio2zarr/core.py

@@ -3,6 +3,8 @@ import contextlib
 import dataclasses
 import logging
 import multiprocessing
+import os
+import os.path
 import threading
 import time
 
@@ -45,6 +47,22 @@ def chunk_aligned_slices(z, n, max_chunks=None):
     return slices
 
 
+def du(path):
+    """
+    Return the total bytes stored at this path.
+    """
+    total = os.path.getsize(path)
+    # pathlib walk method doesn't exist until 3.12 :(
+    for root, dirs, files in os.walk(path):
+        for lst in [dirs, files]:
+            for name in lst:
+                fullname = os.path.join(root, name)
+                size = os.path.getsize(fullname)
+                total += size
+    logger.debug(f"du({path}) = {total}")
+    return total
+
+
 class SynchronousExecutor(cf.Executor):
     def submit(self, fn, /, *args, **kwargs):
         future = cf.Future()