remove biocommons hgvs backend

VariantEffect · Jul 20, 2020 · 188e693 · 188e693
1 parent 2a9671e
commit 188e693
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Showing 4 changed files with 1 addition and 126 deletions.
diff --git a/mavedbconvert/constants.py b/mavedbconvert/constants.py
@@ -2,10 +2,6 @@
 
 from hgvsp import dna
 
-from hgvs.dataproviders import uta
-from hgvs.parser import Parser
-
-
 supported_programs = ("enrich", "enrich2", "empiric")
 extra_na = (
     "None",
@@ -25,22 +21,6 @@
 surrounding_brackets_re = re.compile(r"\((.*)\)")
 dna_re = re.compile(r"[ATCGatcg]+", flags=re.IGNORECASE)
 
-# HGVS
-dummy_ref = "NM_000000000.0"
-hgvs_parser = Parser()
-hdp = None
-
-
-def get_hdp(*args, **kwargs):
-    """Keep a single HDP network connection instance."""
-    global hdp
-    if hdp is None:
-        if "pooling" not in kwargs:
-            kwargs["pooling"] = True
-        hdp = uta.connect(*args, **kwargs)
-    return hdp
-
-
 # HGVSP constants
 hgvsp_nt_pos = "position"
 hgvsp_pro_pos = "position"

diff --git a/mavedbconvert/tests/test_validators.py b/mavedbconvert/tests/test_validators.py
@@ -2,8 +2,6 @@
 
 import pandas as pd
 
-from hgvs.sequencevariant import SequenceVariant
-
 from mavedbconvert import validators, constants, exceptions
 
 
@@ -25,56 +23,7 @@ def test_returns_str_variant(self):
         self.assertIsInstance(self.backend.validate("c.1A>G"), str)
 
 
-class TestHGVSBiocommonsBackend(unittest.TestCase):
-    def setUp(self):
-        self.backend = validators.HGVSBiocommonsBackend("NM_000000001.1")
-
-    def test_validate_hgvs_returns_seqvar_on_success(self):
-        result = self.backend.validate("c.100A>G")
-        self.assertEqual(
-            result,
-            constants.hgvs_parser.parse_hgvs_variant(
-                "{}:c.100A>G".format(self.backend.transcript)
-            ),
-        )
-
-    def test_returns_list_for_multi(self):
-        result = self.backend.validate("c.[1A>G;2A>G]")
-        self.assertListEqual(
-            result,
-            [
-                constants.hgvs_parser.parse_hgvs_variant(
-                    "{}:c.1A>G".format(self.backend.transcript)
-                ),
-                constants.hgvs_parser.parse_hgvs_variant(
-                    "{}:c.2A>G".format(self.backend.transcript)
-                ),
-            ],
-        )
-
-    def test_validate_hgvs_raise_HGVSValidationError(self):
-        with self.assertRaises(exceptions.HGVSValidationError):
-            self.backend.validate("p.1102A>G")
-        with self.assertRaises(exceptions.HGVSValidationError):
-            self.backend.validate("x.102A>G")
-
-    def test_validate_passes_on_special(self):
-        self.backend.validate(constants.enrich2_wildtype)
-        self.backend.validate(constants.enrich2_synonymous)
-
-    def test_validate_hgvs_uses_dummy_ref_if_transcript_not_passed(self):
-        self.assertEqual(
-            validators.HGVSBiocommonsBackend().transcript, constants.dummy_ref
-        )
-
-
 class TestValidateHGVS(unittest.TestCase):
-    def test_uses_biocommons_backend_if_transcript_provided(self):
-        result = validators.validate_variants(
-            ["c.[1A>G;2A>G]"], n_jobs=2, verbose=0, transcript=constants.dummy_ref
-        )
-        self.assertIsInstance(result[0][0], SequenceVariant)
-
     def test_uses_patterns_backend_as_default(self):
         result = validators.validate_variants(["c.[1A>G;2A>G]"], n_jobs=2, verbose=0)
         self.assertIsInstance(result[0], str)

diff --git a/mavedbconvert/validators.py b/mavedbconvert/validators.py
@@ -2,9 +2,6 @@
 
 import hgvsp
 
-from hgvs.sequencevariant import SequenceVariant
-from hgvs.exceptions import HGVSParseError
-
 import numpy as np
 import pandas as pd
 from numpy.testing import assert_array_equal
@@ -59,53 +56,8 @@ def validate(self, variant):
         return variant
 
 
-class HGVSBiocommonsBackend(ValidationBackend):
-    """
-    Backend using the grammar based validation in `hgvs`. Can be slow but is
-    more robust.
-    """
-
-    def __init__(self, transcript=None):
-        self.transcript = transcript or constants.dummy_ref
-
-    def validate(self, variant):
-        """
-        Splits a variant if it is multi-variant to validate each individual
-        variant since `hgvs` does not support multi syntax. Validates each
-        HGVS variant against a set grammar.
-
-        Parameters
-        ----------
-        variant : str
-            HGVS formatted variant string.
-
-        Returns
-        -------
-        list[`SequenceVariant`]
-            List of sequence variants. Singular list if variant was not
-            in multi-variant syntax.
-        """
-        if variant in constants.special_variants:
-            return variant
-        try:
-            seqvars = []
-            for v in utilities.split_variant(variant):
-                seqvar = constants.hgvs_parser.parse_hgvs_variant(
-                    "{}:{}".format(self.transcript, v)
-                )
-                seqvar.validate()
-                seqvars.append(seqvar)
-            return seqvars if len(seqvars) > 1 else seqvars[0]
-        except HGVSParseError as e:
-            raise exceptions.HGVSValidationError(
-                "'{}' is not valid HGVS syntax "
-                "for the following reason: {}".format(variant, e)
-            )
-
-
 def validate_variants(
     variants,
-    transcript=None,
     validation_backend=None,
     n_jobs=1,
     verbose=0,
@@ -118,8 +70,6 @@ def validate_variants(
     ----------
     variants : list[str]
         Variant HGVS_ representations.
-    transcript : str, optional.
-        Transcript the variants reference.
     validation_backend : ValidationBackend
         A parsing backend implementing `validate`.
     n_jobs : int, optional
@@ -135,10 +85,7 @@ def validate_variants(
         Formatted and validated variants.
     """
     if validation_backend is None:
-        if transcript is None:
-            validation_backend = HGVSPatternsBackend()
-        else:
-            validation_backend = HGVSBiocommonsBackend(transcript)
+        validation_backend = HGVSPatternsBackend()
     return Parallel(n_jobs=n_jobs, verbose=verbose, backend=backend)(
         delayed(validation_backend.validate)(variant) for variant in variants
     )

diff --git a/setup.py b/setup.py
@@ -31,7 +31,6 @@
         "tqdm",
         "docopt",
         "hgvsp @ git+https://github.com/VariantEffect/hgvs-patterns",
-        "hgvs",
         "requests",
         "numpy",
         "scipy",