fix: 1) improve error in transform when providing an empty hap file and a --region and 2) allow for calling write() on Genotypes objects without variants

.devcontainer.json

@@ -15,20 +15,31 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "mamba env create -n haptools -f dev-env.yml && conda run -n haptools poetry install",
+	"postCreateCommand": "mamba env create -n haptools -f dev-env.yml && conda run -n haptools poetry config virtualenvs.in-project true && conda run -n haptools poetry install",
 
 	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
-			"extensions": ["ms-python.python"],
+			"extensions": [
+				"ms-python.python",
+				"ms-python.black-formatter"
+			],
 			"settings": {
+				"python.analysis.typeCheckingMode": "off", // TODO: set to "strict"
 				"python.condaPath": "/opt/conda/condabin/conda",
-				"python.defaultInterpreterPath": "/opt/conda/envs/haptools/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"],
+				"python.venvPath": "/workspaces/haptools/.venv",
+				"python.defaultInterpreterPath": "/workspaces/haptools/.venv/bin/python",
+				"python.testing.pytestArgs": [
+					"tests"
+				],
+				"python.testing.pytestEnabled": true,
+				"python.testing.unittestEnabled": false,
 				"terminal.integrated.environmentChangesRelaunch": true,
-				"terminal.integrated.hideOnStartup": "always"
+				"editor.defaultFormatter": "ms-python.black-formatter",
+				"terminal.integrated.hideOnStartup": "always",
+				"files.eol": "\n"
 			}
 		}
 	}

.github/workflows/tests.yml

@@ -39,6 +39,7 @@ jobs:
           auto-activate-base: false
           miniforge-version: latest
           use-mamba: true
+          conda-remove-defaults: "true"
 
       - name: Get Date
         id: get-date

haptools/clump.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from .data import Genotypes, GenotypesVCF, GenotypesTR, GenotypesPLINKTR
+from .data import Genotypes, GenotypesVCF, GenotypesPLINK, GenotypesTR, GenotypesPLINKTR
 
 
 class Variant:

haptools/data/breakpoints.py

@@ -23,7 +23,7 @@
 # This tuple lists the haplotype blocks in a sample, one set for each chromosome
 # Let's define a type alias, "SampleBlocks", for future use...
 SampleBlocks = NewType(
-    "SampleBlocks", "list[npt.NDArray[HapBlock], npt.NDArray[HapBlock]]]"
+    "SampleBlocks", "list[npt.NDArray[HapBlock], npt.NDArray[HapBlock]]]"  # type: ignore
 )
 
 

haptools/data/genotypes.py

@@ -14,7 +14,7 @@
 from cyvcf2 import VCF, Variant
 
 try:
-    import trtools.utils.tr_harmonizer as trh
+    import trtools.utils.tr_harmonizer as trh  # type: ignore
 except ModuleNotFoundError:
     from . import tr_harmonizer as trh
 
@@ -219,7 +219,7 @@ def _variant_arr(self, record: Variant):
         Parameters
         ----------
         record: Variant
-            A cyvcf2.Variant object from which to fetch metadata
+            A Variant object from which to fetch metadata
 
         Returns
         -------
@@ -231,20 +231,20 @@ def _variant_arr(self, record: Variant):
             dtype=self.variants.dtype,
         )
 
-    def _vcf_iter(self, vcf: cyvcf2.VCF, region: str):
+    def _vcf_iter(self, vcf: VCF, region: str):
         """
         Yield all variants within a region in the VCF file.
 
         Parameters
         ----------
         vcf: VCF
-            The cyvcf2.VCF object from which to fetch variant records
+            The VCF object from which to fetch variant records
         region : str, optional
             See documentation for :py:meth:`~.Genotypes.read`
 
         Returns
         -------
-        vcffile : cyvcf2.VCF
+        vcffile : VCF
             Iterable cyvcf2 instance.
         """
         return vcf(region)
@@ -255,8 +255,8 @@ def _return_data(self, variant: Variant):
 
         Parameters
         ----------
-        variant: cyvcf2.Variant
-            A cyvcf2.Variant object from which to fetch genotypes
+        variant: Variant
+            A Variant object from which to fetch genotypes
 
         Returns
         -------
@@ -274,7 +274,7 @@ def _iterate(self, vcf: VCF, region: str = None, variants: set[str] = None):
         Parameters
         ----------
         vcf: VCF
-            The cyvcf2.VCF object from which to fetch variant records
+            The VCF object from which to fetch variant records
         region : str, optional
             See documentation for :py:meth:`~.Genotypes.read`
         variants : set[str], optional
@@ -805,7 +805,13 @@ def write(self):
                     record.samples[sample].phased = self.data[samp_idx, var_idx, 2]
             # write the record to a file
             vcf.write(record)
-        vcf.close()
+        try:
+            vcf.close()
+        except OSError as e:
+            if e.errno == 9 and len(self.variants) == 0:
+                self.log.warning(f"No variants in {self.fname}.")
+            else:
+                raise e
 
 
 class TRRecordHarmonizerRegion(trh.TRRecordHarmonizer):
@@ -909,14 +915,14 @@ def load(
         genotypes.check_phase()
         return genotypes
 
-    def _vcf_iter(self, vcf: cyvcf2.VCF, region: str = None):
+    def _vcf_iter(self, vcf: VCF, region: str = None):
         """
         Collect GTs (trh.TRRecord objects) to iterate over
 
         Parameters
         ----------
         vcf: VCF
-            The cyvcf2.VCF object from which to fetch variant records
+            The VCF object from which to fetch variant records
         region : str, optional
             See documentation for :py:meth:`~.Genotypes.read`
 
@@ -1066,7 +1072,7 @@ def read_samples(self, samples: set[str] = None):
             self.samples = {
                 ct: samp[col_idx]
                 for ct, samp in enumerate(psamples)
-                if (samples is None) or (samp[col_idx] in samples)
+                if len(samp) and ((samples is None) or (samp[col_idx] in samples))
             }
             indices = np.array(list(self.samples.keys()), dtype=np.uint32)
             self.samples = tuple(self.samples.values())
@@ -1289,7 +1295,18 @@ def read(
         super(Genotypes, self).read()
 
         sample_idxs = self.read_samples(samples)
-        pv = pgenlib.PvarReader(bytes(str(self.fname.with_suffix(".pvar")), "utf8"))
+        pvar_fname = bytes(str(self.fname.with_suffix(".pvar")), "utf8")
+        try:
+            pv = pgenlib.PvarReader(pvar_fname)
+        except RuntimeError as e:
+            if e.args[0].decode("utf8").startswith("No variants in"):
+                self.log.warning(f"No variants in {pvar_fname}.")
+                self.data = np.empty(
+                    (len(sample_idxs), 0, (2 + (not self._prephased))), dtype=np.uint8
+                )
+                return
+            else:
+                raise e
 
         with pgenlib.PgenReader(
             bytes(str(self.fname), "utf8"), sample_subset=sample_idxs, pvar=pv
@@ -1544,12 +1561,23 @@ def write(self):
             chunks = len(self.variants)
 
         # write the pgen file
-        pv = pgenlib.PvarReader(bytes(str(self.fname.with_suffix(".pvar")), "utf8"))
+        try:
+            max_allele_ct = pgenlib.PvarReader(
+                bytes(str(self.fname.with_suffix(".pvar")), "utf8")
+            ).get_max_allele_ct()
+        except RuntimeError as e:
+            if len(self.variants) == 0:
+                # write an empty pgen file
+                with open(self.fname, "wb"):
+                    pass
+                return
+            else:
+                raise e
         with pgenlib.PgenWriter(
             filename=bytes(str(self.fname), "utf8"),
             sample_ct=len(self.samples),
             variant_ct=len(self.variants),
-            allele_ct_limit=pv.get_max_allele_ct(),
+            allele_ct_limit=max_allele_ct,
             nonref_flags=False,
             hardcall_phase_present=True,
         ) as pgen:

haptools/data/haplotypes.py

@@ -461,7 +461,7 @@ def extras_order(cls) -> tuple[str]:
         """
         return tuple(extra.name for extra in cls._extras)
 
-    def transform(self, genotypes: GenotypesVCF) -> npt.NDArray[bool]:
+    def transform(self, genotypes: GenotypesVCF) -> npt.NDArray:
         """
         Transform a genotypes matrix via the current haplotype
 
@@ -478,9 +478,9 @@ def transform(self, genotypes: GenotypesVCF) -> npt.NDArray[bool]:
 
         Returns
         -------
-        npt.NDArray[bool]
-            A 2D matrix of shape (num_samples, 2) where each entry in the matrix
-            denotes the presence of the haplotype in one chromosome of a sample
+        npt.NDArray
+            A 2D matrix of shape (num_samples, 2) where each entry in the matrix is a
+            bool denoting the presence of the haplotype in one chromosome of a sample
         """
         var_IDs = self.varIDs
         # ensure the variants in the Genotypes object are ordered according to var_IDs
@@ -1198,12 +1198,16 @@ def __iter__(
         indexed = True
         try:
             haps_file = TabixFile(str(self.fname))
+            if region is not None:
+                haps_file.fetch(region=region, multiple_iterators=True)
         except OSError:
             indexed = False
-        # if the user requested a specific region or subset of haplotypes and the file
+        except ValueError:
+            indexed = False
+        # If the user requested a specific region or subset of haplotypes and the file
         # is indexed, then we should handle it using tabix
         # else, we use a regular text opener - b/c there's no benefit to using tabix
-        if region or (haplotypes and indexed):
+        if (region or haplotypes) and indexed:
             haps_file = TabixFile(str(self.fname))
             metas, extras = self.check_header(list(haps_file.header))
             types = self._get_field_types(extras, metas.get("order"))
@@ -1232,8 +1236,8 @@ def __iter__(
                         )
             haps_file.close()
         else:
-            # the file is not indexed, so we can't assume it's sorted, either
-            # use hook_compressed to automatically handle gz files
+            # The file is not indexed, so we can't assume it's sorted, either
+            # Use hook_compressed to automatically handle gz files
             with self.hook_compressed(self.fname, mode="r") as haps:
                 self.log.info("Not taking advantage of indexing.")
                 header_lines = []

haptools/data/tr_harmonizer.py

@@ -3,6 +3,7 @@
 Handles VCFs generated by various TR genotyping tools
 """
 import re
+import math
 import enum
 import warnings
 from typing import (

haptools/transform.py

@@ -593,6 +593,8 @@ def transform_haps(
             "that the IDs in your .hap file correspond with those you provided. "
             f"Here are the first few missing haplotypes: {diff[:first_few]}"
         )
+    if len(hp.data) == 0:
+        raise ValueError("Didn't load any haplotypes from the .hap file")
 
     log.info("Extracting variants from haplotypes")
     variants = {vr.id for id in hp.type_ids["H"] for vr in hp.data[id].variants}

noxfile.py

@@ -3,9 +3,9 @@
 import shutil
 from pathlib import Path
 
-import nox
-from nox_poetry import Session
-from nox_poetry import session
+import nox  # type: ignore
+from nox_poetry import Session  # type: ignore
+from nox_poetry import session  # type: ignore
 
 
 package = "haptools"

tests/bench_transform.py

@@ -7,6 +7,7 @@
 from datetime import datetime
 
 import click
+import matplotlib
 import numpy as np
 import matplotlib.pyplot as plt
 

tests/test_data.py

@@ -569,6 +569,20 @@ def test_write_genotypes(self):
         fname.with_suffix(".pvar").unlink()
         fname.unlink()
 
+    def test_write_genotypes_empty(self):
+        fname = DATADIR / "test_write.pgen"
+        gts = GenotypesPLINK(fname=fname)
+        gts.data = np.empty((0, 0, 0), dtype=np.uint8)
+        gts.samples = ()
+        gts.variants = np.empty(0, dtype=gts.variants.dtype)
+        gts.write()
+        gts.read()
+
+        # clean up afterwards: delete the files we created
+        fname.with_suffix(".psam").unlink()
+        fname.with_suffix(".pvar").unlink()
+        fname.unlink()
+
     def test_write_genotypes_prephased(self):
         gts = self._get_fake_genotypes_plink()
 
@@ -1851,6 +1865,16 @@ def test_write_ref_alt(self, multiallelic=False):
 
         fname.unlink()
 
+    def test_write_empty(self):
+        fname = Path("test.vcf")
+        gts = GenotypesVCF(fname=fname)
+        gts.samples = ()
+        gts.variants = np.array([], dtype=gts.variants.dtype)
+        gts.data = np.empty((0, 0, 0), dtype=np.uint8)
+        gts.write()
+        gts.read()
+        fname.unlink()
+
     def test_write_multiallelic(self):
         self.test_write_ref_alt(multiallelic=True)
 

tests/test_transform.py

@@ -371,3 +371,42 @@ def test_ancestry_from_bp(capfd):
     captured = capfd.readouterr()
     assert captured.out == ancestry_results
     assert result.exit_code == 0
+
+
+def test_transform_empty_hap(capfd):
+    gt_file = DATADIR / "simple.vcf.gz"
+    hp_file = Path("empty.hap")
+    hp_file_gz = Path("empty.hap.gz")
+    hp_file_idx = Path("empty.hap.gz.tbi")
+
+    # create an empty .hap file
+    with open(hp_file, "w") as f:
+        f.write("")
+
+    # can we run transform with the empty hap file?
+    cmd = f"transform --region 1:10116-10122 {gt_file} {hp_file}"
+    runner = CliRunner()
+    result = runner.invoke(main, cmd.split(" "))
+    captured = capfd.readouterr()
+    assert all(line for line in captured.out.split("\n") if line.startswith("#"))
+    assert result.exit_code != 0
+
+    # now, index the empty hap file and try again
+    cmd = f"index {hp_file}"
+    runner = CliRunner()
+    result = runner.invoke(main, cmd.split(" "), catch_exceptions=False)
+    captured = capfd.readouterr()
+    assert result.exit_code == 0
+    assert hp_file_gz.exists()
+    assert hp_file_idx.exists()
+
+    # what about now? does it still fail?
+    cmd = f"transform --region 1:10116-10122 {gt_file} {hp_file_gz}"
+    runner = CliRunner()
+    result = runner.invoke(main, cmd.split(" "))
+    captured = capfd.readouterr()
+    assert result.exit_code != 0
+
+    hp_file.unlink()
+    hp_file_gz.unlink()
+    hp_file_idx.unlink()