bio2zarr 0.0.5__py3-none-any.whl → 0.0.9__py3-none-any.whl

bio2zarr/vcf_utils.py

@@ -3,8 +3,9 @@ import gzip
 import os
 import pathlib
 import struct
+from collections.abc import Sequence
 from dataclasses import dataclass
-from typing import IO, Any, Dict, Optional, Sequence, Union
+from typing import IO, Any, Optional, Union
 
 import cyvcf2
 import humanfriendly
@@ -75,6 +76,10 @@ def read_bytes_as_tuple(f: IO[Any], fmt: str) -> Sequence[Any]:
 
 @dataclass
 class Region:
+    """
+    A htslib style region, where coordinates are 1-based and inclusive.
+    """
+
     contig: str
     start: Optional[int] = None
     end: Optional[int] = None
@@ -85,7 +90,7 @@ class Region:
             assert self.start > 0
         if self.end is not None:
             self.end = int(self.end)
-            assert self.end > self.start
+            assert self.end >= self.start
 
     def __str__(self):
         s = f"{self.contig}"
@@ -112,6 +117,9 @@ class CSIBin:
     chunks: Sequence[Chunk]
 
 
+RECORD_COUNT_UNKNOWN = np.inf
+
+
 @dataclass
 class CSIIndex:
     min_shift: int
@@ -183,7 +191,7 @@ def get_first_locus_in_bin(csi: CSIIndex, bin: int) -> int:
 
 
 def read_csi(
-    file: PathType, storage_options: Optional[Dict[str, str]] = None
+    file: PathType, storage_options: Optional[dict[str, str]] = None
 ) -> CSIIndex:
     """Parse a CSI file into a `CSIIndex` object.
 
@@ -220,7 +228,9 @@ def read_csi(
             for _ in range(n_ref):
                 n_bin = read_bytes_as_value(f, "<i")
                 seq_bins = []
-                record_count = -1
+                # Distinguish between counts that are zero because the sequence
+                # isn't there, vs counts that aren't in the index.
+                record_count = 0 if n_bin == 0 else RECORD_COUNT_UNKNOWN
                 for _ in range(n_bin):
                     bin, loffset, n_chunk = read_bytes_as_tuple(f, "<IQi")
                     chunks = []
@@ -297,7 +307,7 @@ class TabixIndex:
 
 
 def read_tabix(
-    file: PathType, storage_options: Optional[Dict[str, str]] = None
+    file: PathType, storage_options: Optional[dict[str, str]] = None
 ) -> TabixIndex:
     """Parse a tabix file into a `TabixIndex` object.
 
@@ -336,7 +346,9 @@ def read_tabix(
             for _ in range(header.n_ref):
                 n_bin = read_bytes_as_value(f, "<i")
                 seq_bins = []
-                record_count = -1
+                # Distinguish between counts that are zero because the sequence
+                # isn't there, vs counts that aren't in the index.
+                record_count = 0 if n_bin == 0 else RECORD_COUNT_UNKNOWN
                 for _ in range(n_bin):
                     bin, n_chunk = read_bytes_as_tuple(f, "<Ii")
                     chunks = []
@@ -435,19 +447,16 @@ class IndexedVcf(contextlib.AbstractContextManager):
             if var.POS >= start:
                 yield var
 
-    def _filter_empty(self, regions):
+    def _filter_empty_and_refine(self, regions):
         """
-        Return all regions in the specified list that have one or more records.
-
-        Sometimes with Tabix indexes these seem to crop up:
-
-        - https://github.com/sgkit-dev/bio2zarr/issues/45
-        - https://github.com/sgkit-dev/bio2zarr/issues/120
+        Return all regions in the specified list that have one or more records,
+        and refine the start coordinate of the region to be the actual first coord
         """
         ret = []
         for region in regions:
-            variants = self.variants(region)
-            if next(variants, None) is not None:
+            var = next(self.variants(region), None)
+            if var is not None:
+                region.start = var.POS
                 ret.append(region)
         return ret
 
@@ -527,4 +536,4 @@ class IndexedVcf(contextlib.AbstractContextManager):
             if self.index.record_counts[ri] > 0:
                 regions.append(Region(self.sequence_names[ri]))
 
-        return self._filter_empty(regions)
+        return self._filter_empty_and_refine(regions)

bio2zarr-0.0.9.dist-info/METADATA

@@ -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
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
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+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
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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-0.0.9.dist-info/RECORD

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bio2zarr-0.0.5.dist-info/METADATA

@@ -1,33 +0,0 @@
-Metadata-Version: 2.1
-Name: bio2zarr
-Version: 0.0.5
-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 >=2.17
-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-0.0.5.dist-info/RECORD

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