bio2zarr 0.0.6__py3-none-any.whl → 0.0.10__py3-none-any.whl

bio2zarr/vcf2zarr/verification.py

@@ -0,0 +1,230 @@
+import cyvcf2
+import numpy as np
+import numpy.testing as nt
+import tqdm
+import zarr
+
+from .. import constants
+
+
+def assert_all_missing_float(a):
+    v = np.array(a, dtype=np.float32).view(np.int32)
+    nt.assert_equal(v, constants.FLOAT32_MISSING_AS_INT32)
+
+
+def assert_all_fill_float(a):
+    v = np.array(a, dtype=np.float32).view(np.int32)
+    nt.assert_equal(v, constants.FLOAT32_FILL_AS_INT32)
+
+
+def assert_all_missing_int(a):
+    v = np.array(a, dtype=int)
+    nt.assert_equal(v, constants.INT_MISSING)
+
+
+def assert_all_fill_int(a):
+    v = np.array(a, dtype=int)
+    nt.assert_equal(v, constants.INT_FILL)
+
+
+def assert_all_missing_string(a):
+    nt.assert_equal(a, constants.STR_MISSING)
+
+
+def assert_all_fill_string(a):
+    nt.assert_equal(a, constants.STR_FILL)
+
+
+def assert_all_fill(zarr_val, vcf_type):
+    if vcf_type == "Integer":
+        assert_all_fill_int(zarr_val)
+    elif vcf_type in ("String", "Character"):
+        assert_all_fill_string(zarr_val)
+    elif vcf_type == "Float":
+        assert_all_fill_float(zarr_val)
+    else:  # pragma: no cover
+        assert False  # noqa PT015
+
+
+def assert_all_missing(zarr_val, vcf_type):
+    if vcf_type == "Integer":
+        assert_all_missing_int(zarr_val)
+    elif vcf_type in ("String", "Character"):
+        assert_all_missing_string(zarr_val)
+    elif vcf_type == "Flag":
+        assert zarr_val == False  # noqa 712
+    elif vcf_type == "Float":
+        assert_all_missing_float(zarr_val)
+    else:  # pragma: no cover
+        assert False  # noqa PT015
+
+
+def assert_info_val_missing(zarr_val, vcf_type):
+    assert_all_missing(zarr_val, vcf_type)
+
+
+def assert_format_val_missing(zarr_val, vcf_type):
+    assert_info_val_missing(zarr_val, vcf_type)
+
+
+# Note: checking exact equality may prove problematic here
+# but we should be deterministically storing what cyvcf2
+# provides, which should compare equal.
+
+
+def assert_info_val_equal(vcf_val, zarr_val, vcf_type):
+    assert vcf_val is not None
+    if vcf_type in ("String", "Character"):
+        split = list(vcf_val.split(","))
+        k = len(split)
+        if isinstance(zarr_val, str):
+            assert k == 1
+            # Scalar
+            assert vcf_val == zarr_val
+        else:
+            nt.assert_equal(split, zarr_val[:k])
+            assert_all_fill(zarr_val[k:], vcf_type)
+
+    elif isinstance(vcf_val, tuple):
+        vcf_missing_value_map = {
+            "Integer": constants.INT_MISSING,
+            "Float": constants.FLOAT32_MISSING,
+        }
+        v = [vcf_missing_value_map[vcf_type] if x is None else x for x in vcf_val]
+        missing = np.array([j for j, x in enumerate(vcf_val) if x is None], dtype=int)
+        a = np.array(v)
+        k = len(a)
+        # We are checking for int missing twice here, but it's necessary to have
+        # a separate check for floats because different NaNs compare equal
+        nt.assert_equal(a, zarr_val[:k])
+        assert_all_missing(zarr_val[missing], vcf_type)
+        if k < len(zarr_val):
+            assert_all_fill(zarr_val[k:], vcf_type)
+    else:
+        # Scalar
+        zarr_val = np.array(zarr_val, ndmin=1)
+        assert len(zarr_val.shape) == 1
+        assert vcf_val == zarr_val[0]
+        if len(zarr_val) > 1:
+            assert_all_fill(zarr_val[1:], vcf_type)
+
+
+def assert_format_val_equal(vcf_val, zarr_val, vcf_type):
+    assert vcf_val is not None
+    assert isinstance(vcf_val, np.ndarray)
+    if vcf_type in ("String", "Character"):
+        assert len(vcf_val) == len(zarr_val)
+        for v, z in zip(vcf_val, zarr_val):
+            split = list(v.split(","))
+            # Note: deliberately duplicating logic here between this and the
+            # INFO col above to make sure all combinations are covered by tests
+            k = len(split)
+            if k == 1:
+                assert v == z
+            else:
+                nt.assert_equal(split, z[:k])
+                assert_all_fill(z[k:], vcf_type)
+    else:
+        assert vcf_val.shape[0] == zarr_val.shape[0]
+        if len(vcf_val.shape) == len(zarr_val.shape) + 1:
+            assert vcf_val.shape[-1] == 1
+            vcf_val = vcf_val[..., 0]
+        assert len(vcf_val.shape) <= 2
+        assert len(vcf_val.shape) == len(zarr_val.shape)
+        if len(vcf_val.shape) == 2:
+            k = vcf_val.shape[1]
+            if zarr_val.shape[1] != k:
+                assert_all_fill(zarr_val[:, k:], vcf_type)
+                zarr_val = zarr_val[:, :k]
+        assert vcf_val.shape == zarr_val.shape
+        if vcf_type == "Integer":
+            vcf_val[vcf_val == constants.VCF_INT_MISSING] = constants.INT_MISSING
+            vcf_val[vcf_val == constants.VCF_INT_FILL] = constants.INT_FILL
+        elif vcf_type == "Float":
+            nt.assert_equal(vcf_val.view(np.int32), zarr_val.view(np.int32))
+
+        nt.assert_equal(vcf_val, zarr_val)
+
+
+def verify(vcf_path, zarr_path, show_progress=False):
+    store = zarr.DirectoryStore(zarr_path)
+
+    root = zarr.group(store=store)
+    pos = root["variant_position"][:]
+    allele = root["variant_allele"][:]
+    chrom = root["contig_id"][:][root["variant_contig"][:]]
+    vid = root["variant_id"][:]
+    call_genotype = None
+    if "call_genotype" in root:
+        call_genotype = iter(root["call_genotype"])
+
+    vcf = cyvcf2.VCF(vcf_path)
+    format_headers = {}
+    info_headers = {}
+    for h in vcf.header_iter():
+        if h["HeaderType"] == "FORMAT":
+            format_headers[h["ID"]] = h
+        if h["HeaderType"] == "INFO":
+            info_headers[h["ID"]] = h
+
+    format_fields = {}
+    info_fields = {}
+    for colname in root.keys():
+        if colname.startswith("call") and not colname.startswith("call_genotype"):
+            vcf_name = colname.split("_", 1)[1]
+            vcf_type = format_headers[vcf_name]["Type"]
+            format_fields[vcf_name] = vcf_type, iter(root[colname])
+        if colname.startswith("variant"):
+            name = colname.split("_", 1)[1]
+            if name.isupper():
+                vcf_type = info_headers[name]["Type"]
+                info_fields[name] = vcf_type, iter(root[colname])
+
+    first_pos = next(vcf).POS
+    start_index = np.searchsorted(pos, first_pos)
+    assert pos[start_index] == first_pos
+    vcf = cyvcf2.VCF(vcf_path)
+    if show_progress:
+        iterator = tqdm.tqdm(vcf, desc="  Verify", total=vcf.num_records)  # NEEDS TEST
+    else:
+        iterator = vcf
+    for j, row in enumerate(iterator, start_index):
+        assert chrom[j] == row.CHROM
+        assert pos[j] == row.POS
+        assert vid[j] == ("." if row.ID is None else row.ID)
+        assert allele[j, 0] == row.REF
+        k = len(row.ALT)
+        nt.assert_array_equal(allele[j, 1 : k + 1], row.ALT)
+        assert np.all(allele[j, k + 1 :] == "")
+        # TODO FILTERS
+
+        if call_genotype is None:
+            val = None
+            try:
+                val = row.format("GT")
+            except KeyError:
+                pass
+            assert val is None
+        else:
+            gt = row.genotype.array()
+            gt_zarr = next(call_genotype)
+            gt_vcf = gt[:, :-1]
+            # NOTE cyvcf2 remaps genotypes automatically
+            # into the same missing/pad encoding that sgkit uses.
+            nt.assert_array_equal(gt_zarr, gt_vcf)
+
+        for name, (vcf_type, zarr_iter) in info_fields.items():
+            vcf_val = row.INFO.get(name, None)
+            zarr_val = next(zarr_iter)
+            if vcf_val is None:
+                assert_info_val_missing(zarr_val, vcf_type)
+            else:
+                assert_info_val_equal(vcf_val, zarr_val, vcf_type)
+
+        for name, (vcf_type, zarr_iter) in format_fields.items():
+            vcf_val = row.format(name)
+            zarr_val = next(zarr_iter)
+            if vcf_val is None:
+                assert_format_val_missing(zarr_val, vcf_type)
+            else:
+                assert_format_val_equal(vcf_val, zarr_val, vcf_type)

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 = []
@@ -429,25 +441,22 @@ class IndexedVcf(contextlib.AbstractContextManager):
         return sum(1 for _ in self.variants(region))
 
     def variants(self, region):
-        # Need to filter because of indels overlapping the region
         start = 1 if region.start is None else region.start
         for var in self.vcf(str(region)):
+            # Need to filter because of indels overlapping the region
             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-0.0.10.dist-info/METADATA

@@ -0,0 +1,250 @@
+Metadata-Version: 2.1
+Name: bio2zarr
+Version: 0.0.10
+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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+Project-URL: repository, https://github.com/sgkit-dev/bio2zarr
+Project-URL: documentation, https://sgkit-dev.github.io/bio2zarr/
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Operating System :: MacOS
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+Classifier: Programming Language :: Python
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+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
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+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)
+[![Coverage Status](https://coveralls.io/repos/github/sgkit-dev/bio2zarr/badge.svg)](https://coveralls.io/github/sgkit-dev/bio2zarr)
+
+
+# bio2zarr
+Convert bioinformatics file formats to Zarr
+
+See the [documentation](https://sgkit-dev.github.io/bio2zarr/) for details.

bio2zarr-0.0.10.dist-info/RECORD

@@ -0,0 +1,20 @@
+bio2zarr/__init__.py,sha256=KiUGyya-9RHNcBldB8Lc1g3rP3CRjaL-5Olben0_6qA,49
+bio2zarr/__main__.py,sha256=wUKNNps8MAAEpMvLgVaI449eKyfr7Jpk2mMtYbNl4Ek,531
+bio2zarr/_version.py,sha256=IBUgg21Ew0JtWj9Z6eN1r4zXlrNseQQNV4zo-nYzlEY,413
+bio2zarr/cli.py,sha256=Bv4k9V-5HJVVbqBMiYLWz5IQyILQ0bTicqgkQrr9hd0,13209
+bio2zarr/constants.py,sha256=QjbtFeBUZ-XqG35ZFIFj8EYrta_EwUkC2B5VGRP7oQs,425
+bio2zarr/core.py,sha256=3UFh7nKB3CbAIaJV3wgoqlkRy1M235C2vz7Iua73qwM,9234
+bio2zarr/plink.py,sha256=huXMlxQ5C3gPmOYCavA-QW7PzaV48I2lo80cQqHT1wY,6768
+bio2zarr/provenance.py,sha256=c_Z__QbWkLS0Rfa8D7LgEhtStng_zRMJX8comaDXIkw,142
+bio2zarr/typing.py,sha256=BYxhL16sKRoNxa6amf6AYxvt5Ke9qzv2np_kOT_zPJo,79
+bio2zarr/vcf_utils.py,sha256=b3Ti1AFXFlK7S1mu6jotqHPrujCIQXBKIHH8yIzd3zk,17781
+bio2zarr/vcf2zarr/__init__.py,sha256=0_of1iGzIDhvti49Gbcgd47oP63mKvouk9uLgKgiwoQ,791
+bio2zarr/vcf2zarr/icf.py,sha256=BJKPJDeqP8QtVz7ebm6NQQgvsba8H-JLsNEz4whOxsw,41559
+bio2zarr/vcf2zarr/vcz.py,sha256=sy8VVYuOntMuPs5gUwQx6IA39_Gl_YFW2h-CeRyQw2A,36865
+bio2zarr/vcf2zarr/verification.py,sha256=6xcBy-cJLaQz2Qj2crffXFMjUG-H7z637Csxe5ZCmds,7898
+bio2zarr-0.0.10.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+bio2zarr-0.0.10.dist-info/METADATA,sha256=7su1JbkFtR7eDjq2Rp5A8CjP9KnvwWaDS6bPH43Z2qI,14850
+bio2zarr-0.0.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+bio2zarr-0.0.10.dist-info/entry_points.txt,sha256=3adtRrClMpjatEbiYqK5bm9WHA2PaJN5hK-Cs_zkpaI,97
+bio2zarr-0.0.10.dist-info/top_level.txt,sha256=ouAvp3u9N25eKrQbN8BCDLPcWWQLhtlgdHKu8AtEj5Q,9
+bio2zarr-0.0.10.dist-info/RECORD,,

bio2zarr-0.0.10.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+vcf2zarr = bio2zarr.cli:vcf2zarr_main
+vcfpartition = bio2zarr.cli:vcfpartition