From 012ce1e09f273d5d27cd3d9ef8deadc5fe8734c8 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 24 Mar 2023 11:27:45 -0700
Subject: [PATCH 1/4] feat: allow user to provide own chain file for pyliftover
 (#136)

- Can set via UTADatabase parameters, environment variables
  (LIFTOVER_CHAIN_37_TO_38, LIFTOVER_CHAIN_38_TO_37), else will use
pyliftover default methods to download from UCSC
---
 cool_seq_tool/data_sources/uta_database.py | 38 +++++++++++++++++++---
 cool_seq_tool/version.py                   |  2 +-
 2 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/cool_seq_tool/data_sources/uta_database.py b/cool_seq_tool/data_sources/uta_database.py
index faa453d2..089b0a3e 100644
--- a/cool_seq_tool/data_sources/uta_database.py
+++ b/cool_seq_tool/data_sources/uta_database.py
@@ -21,25 +21,53 @@
 # use `bound` to upper-bound UTADatabase or child classes
 UTADatabaseType = TypeVar("UTADatabaseType", bound="UTADatabase")
 
+# Environment variables for paths to chain files for pyliftover
+LIFTOVER_CHAIN_37_TO_38 = environ.get("LIFTOVER_CHAIN_37_TO_38")
+LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
+
 
 class UTADatabase:
     """Class for connecting and querying UTA database."""
 
-    def __init__(self, db_url: str = UTA_DB_URL, db_pwd: str = "") -> None:
+    def __init__(
+        self,
+        db_url: str = UTA_DB_URL,
+        db_pwd: str = "",
+        chain_file_37_to_38: Optional[str] = None,
+        chain_file_38_to_37: Optional[str] = None
+    ) -> None:
         """Initialize DB class. Downstream libraries should use the create()
         method to construct a new instance: await UTADatabase.create()
 
-        :param str db_url: PostgreSQL connection URL
+        :param db_url: PostgreSQL connection URL
             Format: `driver://user:pass@host/database/schema`
-        :param str db_pwd: User's password for uta database
+        :param db_pwd: User's password for uta database
+        :param chain_file_37_to_38: Optional path to chain file for 37 to 38 assembly.
+            This is used for pyliftover. If this is not provided, will check to see if
+            LIFTOVER_CHAIN_37_TO_38 env var is set. If neither is provided, will allow
+            pyliftover to download a chain file from UCSC
+        :param chain_file_38_to_37: Optional path to chain file for 38 to 37 assembly.
+            This is used for pyliftover. If this is not provided, will check to see if
+            LIFTOVER_CHAIN_38_TO_37 env var is set. If neither is provided, will allow
+            pyliftover to download a chain file from UCSC
         """
         self.schema = None
         self.db_url = db_url
         self.db_pwd = db_pwd
         self._connection_pool = None
         self.args = self._get_conn_args()
-        self.liftover_37_to_38 = LiftOver("hg19", "hg38")
-        self.liftover_38_to_37 = LiftOver("hg38", "hg19")
+
+        chain_file_37_to_38 = chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38
+        if chain_file_37_to_38:
+            self.liftover_37_to_38 = LiftOver(chain_file_37_to_38)
+        else:
+            self.liftover_37_to_38 = LiftOver("hg19", "hg38")
+
+        chain_file_38_to_37 = chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37
+        if chain_file_38_to_37:
+            self.liftover_38_to_37 = LiftOver(chain_file_38_to_37)
+        else:
+            self.liftover_38_to_37 = LiftOver("hg38", "hg19")
 
     @staticmethod
     def _update_db_url(db_pwd: str, db_url: str) -> str:
diff --git a/cool_seq_tool/version.py b/cool_seq_tool/version.py
index 9cb17e79..c11f861a 100644
--- a/cool_seq_tool/version.py
+++ b/cool_seq_tool/version.py
@@ -1 +1 @@
-__version__ = "0.1.8"
+__version__ = "0.1.9"

From ab8a276e9e941d7dd4e0fc425a7aa50e1686800e Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 31 Mar 2023 08:17:30 -0700
Subject: [PATCH 2/4] refactor!: SeqRepoAccess extends vrs-python's
 SeqRepoDataProxy class (#138)

- SeqRepoAccess translate_identifier method: parameter changed from
  target_namespace --> target_namespaces
- SeqRepoAccess aliases method: renamed to translate_alias
---
 README.md                                    |  2 +-
 cool_seq_tool/__init__.py                    |  3 +-
 cool_seq_tool/cool_seq_tool.py               | 29 +++++++-------
 cool_seq_tool/data_sources/seqrepo_access.py | 41 +++++++++-----------
 cool_seq_tool/version.py                     |  2 +-
 tests/unit/conftest.py                       | 12 ++++++
 tests/unit/test_alignment_mapper.py          |  7 ++--
 tests/unit/test_mane_transcript.py           |  4 +-
 tests/unit/test_seqrepo_access.py            | 16 ++++----
 9 files changed, 63 insertions(+), 53 deletions(-)
 create mode 100644 tests/unit/conftest.py

diff --git a/README.md b/README.md
index 3f6fe996..854bdfab 100644
--- a/README.md
+++ b/README.md
@@ -71,7 +71,7 @@ If you do not wish to use the default, you must set the environment variable `UT
 #### SeqRepo
 `cool-seq-tool` relies on [seqrepo](https://github.com/biocommons/biocommons.seqrepo), which you must download yourself.
 
-Use the `SEQREPO_DATA_PATH` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
+Use the `SEQREPO_ROOT_DIR` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
 
 From the _root_ directory:
 ```
diff --git a/cool_seq_tool/__init__.py b/cool_seq_tool/__init__.py
index e7cb917f..8641a4e4 100644
--- a/cool_seq_tool/__init__.py
+++ b/cool_seq_tool/__init__.py
@@ -16,8 +16,7 @@
 
 UTA_DB_URL = environ.get("UTA_DB_URL",
                          "postgresql://uta_admin@localhost:5433/uta/uta_20210129")
-SEQREPO_DATA_PATH = Path(environ.get("SEQREPO_DATA_PATH",
-                                     "/usr/local/share/seqrepo/latest"))
+SEQREPO_ROOT_DIR = environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
 TRANSCRIPT_MAPPINGS_PATH = Path(environ.get("TRANSCRIPT_MAPPINGS_PATH",
                                             f"{APP_ROOT}/data/transcript_mapping.tsv"))
 
diff --git a/cool_seq_tool/cool_seq_tool.py b/cool_seq_tool/cool_seq_tool.py
index 90a67235..b75553b3 100644
--- a/cool_seq_tool/cool_seq_tool.py
+++ b/cool_seq_tool/cool_seq_tool.py
@@ -3,17 +3,17 @@
 from typing import Optional, Union, List, Tuple, Dict
 from pathlib import Path
 
+from biocommons.seqrepo import SeqRepo
 from gene.query import QueryHandler as GeneQueryHandler
 
-from cool_seq_tool import logger
+from cool_seq_tool import logger, SEQREPO_ROOT_DIR
 from cool_seq_tool.data_sources.alignment_mapper import AlignmentMapper
 from cool_seq_tool.schemas import Assembly, GenomicData, TranscriptExonData, \
     ResidueMode, GenomicDataResponse, ServiceMeta, TranscriptExonDataResponse
 from cool_seq_tool.data_sources import MANETranscript, MANETranscriptMappings,\
     SeqRepoAccess, TranscriptMappings, UTADatabase, GeneNormalizer
-from cool_seq_tool import SEQREPO_DATA_PATH, \
-    TRANSCRIPT_MAPPINGS_PATH, LRG_REFSEQGENE_PATH, MANE_SUMMARY_PATH, \
-    UTA_DB_URL
+from cool_seq_tool import TRANSCRIPT_MAPPINGS_PATH, LRG_REFSEQGENE_PATH, \
+    MANE_SUMMARY_PATH, UTA_DB_URL
 from cool_seq_tool.version import __version__
 
 
@@ -21,33 +21,36 @@ class CoolSeqTool:
     """Class to initialize data sources."""
 
     def __init__(
-        self, seqrepo_data_path: Path = SEQREPO_DATA_PATH,
+        self,
         transcript_file_path: Path = TRANSCRIPT_MAPPINGS_PATH,
         lrg_refseqgene_path: Path = LRG_REFSEQGENE_PATH,
         mane_data_path: Path = MANE_SUMMARY_PATH,
         db_url: str = UTA_DB_URL, db_pwd: str = "",
-        gene_query_handler: GeneQueryHandler = None,
-        gene_db_url: str = "", gene_db_region: str = "us-east-2"
+        gene_query_handler: Optional[GeneQueryHandler] = None,
+        gene_db_url: str = "", gene_db_region: str = "us-east-2",
+        sr: Optional[SeqRepo] = None
     ) -> None:
         """Initialize CoolSeqTool class
 
-        :param Path seqrepo_data_path: The path to the seqrepo directory.
         :param Path transcript_file_path: The path to transcript_mappings.tsv
         :param Path lrg_refseqgene_path: The path to LRG_RefSeqGene
         :param Path mane_data_path: Path to RefSeq MANE summary data
         :param str db_url: PostgreSQL connection URL
             Format: `driver://user:pass@host/database/schema`
         :param str db_pwd: User's password for uta database
-        :param GeneQueryHandler gene_query_handler: Gene normalizer query handler
-            instance. If this is provided, will use a current instance. If this is not
-            provided, will create a new instance.
+        :param Optional[GeneQueryHandler] gene_query_handler: Gene normalizer query
+            handler instance. If this is provided, will use a current instance. If this
+            is not provided, will create a new instance.
         :param str gene_db_url: URL to gene normalizer dynamodb. Only used when
             `gene_query_handler` is `None`.
         :param str gene_db_region: AWS region for gene normalizer db. Only used when
             `gene_query_handler` is `None`.
+        :param Optional[SeqRepo] sr: SeqRepo instance. If this is not provided, will
+            create a new instance.
         """
-        self.seqrepo_access = SeqRepoAccess(
-            seqrepo_data_path=seqrepo_data_path)
+        if not sr:
+            sr = SeqRepo(root_dir=SEQREPO_ROOT_DIR)
+        self.seqrepo_access = SeqRepoAccess(sr)
         self.transcript_mappings = TranscriptMappings(
             transcript_file_path=transcript_file_path,
             lrg_refseqgene_path=lrg_refseqgene_path)
diff --git a/cool_seq_tool/data_sources/seqrepo_access.py b/cool_seq_tool/data_sources/seqrepo_access.py
index 4e3fc83b..ef9e0f05 100644
--- a/cool_seq_tool/data_sources/seqrepo_access.py
+++ b/cool_seq_tool/data_sources/seqrepo_access.py
@@ -1,28 +1,22 @@
 """A module for accessing SeqRepo."""
 from typing import Optional, List, Tuple, Union
 from os import environ
-from pathlib import Path
 
-from biocommons.seqrepo import SeqRepo
+from ga4gh.vrs.dataproxy import SeqRepoDataProxy
 
 from cool_seq_tool.schemas import ResidueMode
-from cool_seq_tool import SEQREPO_DATA_PATH, logger
+from cool_seq_tool import logger
 from cool_seq_tool.data_sources.residue_mode import get_inter_residue_pos
 
 
-class SeqRepoAccess:
+class SeqRepoAccess(SeqRepoDataProxy):
     """The SeqRepoAccess class."""
 
-    def __init__(self, seqrepo_data_path: Path = SEQREPO_DATA_PATH) -> None:
-        """Initialize the SeqRepoAccess class.
-        :param Path seqrepo_data_path: The path to the seqrepo directory.
-        """
-        environ["SEQREPO_LRU_CACHE_MAXSIZE"] = "none"
-        self.seqrepo_client = SeqRepo(seqrepo_data_path)
+    environ["SEQREPO_LRU_CACHE_MAXSIZE"] = "none"
 
     def get_reference_sequence(
-            self, ac: str, start: Optional[int] = None, end: Optional[int] = None,
-            residue_mode: str = ResidueMode.RESIDUE
+        self, ac: str, start: Optional[int] = None, end: Optional[int] = None,
+        residue_mode: str = ResidueMode.RESIDUE
     ) -> Tuple[str, Optional[str]]:
         """Get reference sequence for an accession given a start and end position.
         If `start` and `end` are not given, it will return the entire reference sequence
@@ -45,7 +39,7 @@ def get_reference_sequence(
                 if start == end:
                     end += 1
         try:
-            sequence = self.seqrepo_client.fetch(ac, start=start, end=end)
+            sequence = self.sr.fetch(ac, start=start, end=end)
         except KeyError:
             msg = f"Accession, {ac}, not found in SeqRepo"
             logger.warning(msg)
@@ -77,7 +71,7 @@ def get_reference_sequence(
             return sequence, None
 
     def translate_identifier(
-            self, ac: str, target_namespace: Optional[Union[str, List[str]]] = None
+        self, ac: str, target_namespaces: Optional[Union[str, List[str]]] = None
     ) -> Tuple[List[str], Optional[str]]:
         """Return list of identifiers for accession.
 
@@ -86,8 +80,8 @@ def translate_identifier(
         :return: List of identifiers, warning
         """
         try:
-            ga4gh_identifiers = self.seqrepo_client.translate_identifier(
-                ac, target_namespaces=target_namespace)
+            ga4gh_identifiers = self.sr.translate_identifier(
+                ac, target_namespaces=target_namespaces)
         except KeyError:
             msg = f"SeqRepo unable to get translated identifiers for {ac}"
             logger.warning(msg)
@@ -95,22 +89,23 @@ def translate_identifier(
         else:
             return ga4gh_identifiers, None
 
-    def aliases(self,
-                input_str: str) -> Tuple[List[Optional[str]], Optional[str]]:
+    def translate_alias(
+        self, input_str: str
+    ) -> Tuple[List[Optional[str]], Optional[str]]:
         """Get aliases for a given input.
 
         :param str input_str: Input to get aliases for
         :return: List of aliases, warning
         """
         try:
-            return self.seqrepo_client.translate_alias(input_str), None
+            return self.sr.translate_alias(input_str), None
         except KeyError:
             msg = f"SeqRepo could not translate alias {input_str}"
             logger.warning(msg)
             return [], msg
 
     def chromosome_to_acs(
-            self, chromosome: str
+        self, chromosome: str
     ) -> Tuple[Optional[List[str]], Optional[str]]:
         """Get accessions for a chromosome
 
@@ -119,8 +114,8 @@ def chromosome_to_acs(
         """
         acs = []
         for assembly in ["GRCh38", "GRCh37"]:
-            tmp_acs = self.translate_identifier(f"{assembly}:chr{chromosome}",
-                                                target_namespace="refseq")[0]
+            tmp_acs, _ = self.translate_identifier(f"{assembly}:chr{chromosome}",
+                                                   target_namespaces="refseq")
             for ac in tmp_acs:
                 acs.append(ac.split("refseq:")[-1])
         if acs:
@@ -134,7 +129,7 @@ def ac_to_chromosome(self, ac: str) -> Tuple[Optional[str], Optional[str]]:
         :param str ac: Accession
         :return: Chromosome, warning
         """
-        aliases, warning = self.aliases(ac)
+        aliases, _ = self.translate_alias(ac)
         aliases = ([a.split(":")[-1] for a in aliases
                     if a.startswith("GRCh") and "." not in a and "chr" not in a] or [None])[0]  # noqa: E501
         if aliases is None:
diff --git a/cool_seq_tool/version.py b/cool_seq_tool/version.py
index c11f861a..569b1212 100644
--- a/cool_seq_tool/version.py
+++ b/cool_seq_tool/version.py
@@ -1 +1 @@
-__version__ = "0.1.9"
+__version__ = "0.1.10"
diff --git a/tests/unit/conftest.py b/tests/unit/conftest.py
new file mode 100644
index 00000000..4a7bd3b1
--- /dev/null
+++ b/tests/unit/conftest.py
@@ -0,0 +1,12 @@
+"""Provide utilities for test cases."""
+from biocommons.seqrepo import SeqRepo
+import pytest
+
+from cool_seq_tool import SEQREPO_ROOT_DIR
+from cool_seq_tool.data_sources import SeqRepoAccess
+
+
+@pytest.fixture(scope="session")
+def test_seqrepo_access():
+    """Create SeqRepoAccess test fixture"""
+    return SeqRepoAccess(SeqRepo(root_dir=SEQREPO_ROOT_DIR))
diff --git a/tests/unit/test_alignment_mapper.py b/tests/unit/test_alignment_mapper.py
index d01c03b6..6d155b25 100644
--- a/tests/unit/test_alignment_mapper.py
+++ b/tests/unit/test_alignment_mapper.py
@@ -1,15 +1,14 @@
 """Module for testing the Alignment Mapper class"""
 import pytest
 
-from cool_seq_tool.data_sources import AlignmentMapper, SeqRepoAccess, \
-    TranscriptMappings, UTADatabase
+from cool_seq_tool.data_sources import AlignmentMapper, TranscriptMappings, UTADatabase
 from cool_seq_tool.schemas import Assembly, ResidueMode
 
 
 @pytest.fixture(scope="module")
-def test_alignment_mapper():
+def test_alignment_mapper(test_seqrepo_access):
     """Build AlignmentMapper test fixture"""
-    return AlignmentMapper(SeqRepoAccess(), TranscriptMappings(), UTADatabase())
+    return AlignmentMapper(test_seqrepo_access, TranscriptMappings(), UTADatabase())
 
 
 @pytest.fixture(scope="module")
diff --git a/tests/unit/test_mane_transcript.py b/tests/unit/test_mane_transcript.py
index f08ced33..e9639910 100644
--- a/tests/unit/test_mane_transcript.py
+++ b/tests/unit/test_mane_transcript.py
@@ -12,9 +12,9 @@
 
 
 @pytest.fixture(scope="module")
-def test_mane_transcript():
+def test_mane_transcript(test_seqrepo_access):
     """Build mane transcript test fixture."""
-    return MANETranscript(SeqRepoAccess(), TranscriptMappings(),
+    return MANETranscript(test_seqrepo_access, TranscriptMappings(),
                           MANETranscriptMappings(), UTADatabase(), GeneNormalizer())
 
 
diff --git a/tests/unit/test_seqrepo_access.py b/tests/unit/test_seqrepo_access.py
index dd886bb1..d1a31f25 100644
--- a/tests/unit/test_seqrepo_access.py
+++ b/tests/unit/test_seqrepo_access.py
@@ -1,13 +1,15 @@
 """Module for testing seqrepo access class"""
 import pytest
+from biocommons.seqrepo import SeqRepo
 
+from cool_seq_tool import SEQREPO_ROOT_DIR
 from cool_seq_tool.data_sources import SeqRepoAccess
 
 
 @pytest.fixture(scope="module")
 def test_seqrepo_access():
     """Create SeqRepoAccess test fixture"""
-    return SeqRepoAccess()
+    return SeqRepoAccess(SeqRepo(root_dir=SEQREPO_ROOT_DIR))
 
 
 def test_get_reference_sequence(test_seqrepo_access):
@@ -51,11 +53,11 @@ def test_translate_identifier(test_seqrepo_access):
     """Test that translate_identifier method works correctly"""
     expected = (["ga4gh:SQ.ijXOSP3XSsuLWZhXQ7_TJ5JXu4RJO6VT"], None)
     resp = test_seqrepo_access.translate_identifier(
-        "NM_152263.3", target_namespace="ga4gh")
+        "NM_152263.3", target_namespaces="ga4gh")
     assert resp == expected
 
     resp = test_seqrepo_access.translate_identifier(
-        "refseq:NM_152263.3", target_namespace="ga4gh")
+        "refseq:NM_152263.3", target_namespaces="ga4gh")
     assert resp == expected
 
     resp = test_seqrepo_access.translate_identifier("refseq:NM_152263.3")
@@ -81,20 +83,20 @@ def test_translate_identifier(test_seqrepo_access):
 def test_aliases(test_seqrepo_access):
     """Test that aliases method works correctly"""
     expected = (["ga4gh:SQ.ijXOSP3XSsuLWZhXQ7_TJ5JXu4RJO6VT"], None)
-    resp = test_seqrepo_access.aliases("NM_152263.3")
+    resp = test_seqrepo_access.translate_alias("NM_152263.3")
     assert len(resp[0]) > 0
     assert resp[1] is None
     assert expected[0][0] in resp[0]
 
-    resp = test_seqrepo_access.aliases("NC_000002.12")
+    resp = test_seqrepo_access.translate_alias("NC_000002.12")
     assert len(resp[0]) > 0
     assert resp[1] is None
     assert "GRCh38:2" in resp[0]
 
-    resp = test_seqrepo_access.aliases("refseq_152263.3")
+    resp = test_seqrepo_access.translate_alias("refseq_152263.3")
     assert resp == ([], "SeqRepo could not translate alias refseq_152263.3")
 
-    resp = test_seqrepo_access.aliases("GRCh38:2")
+    resp = test_seqrepo_access.translate_alias("GRCh38:2")
     assert resp == ([], "SeqRepo could not translate alias GRCh38:2")
 
 

From fe798ef8542f4a46b538cd5d47199da03c8af276 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Fri, 31 Mar 2023 08:30:54 -0700
Subject: [PATCH 3/4] build: update dependencies (#139)

- Add ga4gh.vrs
- Separate out dev/tests dependencies in setup.cfg
---
 Pipfile              |   5 +-
 README.md            |   4 +-
 requirements-dev.txt | 193 +++++++++++++++++--------------------------
 requirements.txt     | 104 +++++++++++------------
 setup.cfg            |  21 +++--
 5 files changed, 144 insertions(+), 183 deletions(-)

diff --git a/Pipfile b/Pipfile
index 792cffe5..3046fffb 100644
--- a/Pipfile
+++ b/Pipfile
@@ -15,6 +15,7 @@ pydantic = "*"
 fastapi = "*"
 uvicorn = "*"
 gene-normalizer = "*"
+"ga4gh.vrs" = "*"
 
 [dev-packages]
 cool_seq_tool = {editable = true, path = "."}
@@ -25,11 +26,9 @@ flake8-docstrings = "*"
 flake8-annotations = "*"
 flake8-quotes = "*"
 flake8-import-order = "*"
-coverage = "*"
 pytest-cov = "*"
-coveralls = "*"
-jupyterlab = "*"
 pytest-asyncio = "==0.18.3"
 ipython = "*"
+ipykernel = "*"
 psycopg2-binary = "*"
 mock = "*"
diff --git a/README.md b/README.md
index 854bdfab..04860f54 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@ The **cool-seq-tool** provides:
 ### pip
 
 ```commandline
-pip install cool-seq-tool
+pip install cool-seq-tool[dev,tests]
 ```
 
 ### Development
@@ -30,7 +30,7 @@ Install backend dependencies and enter Pipenv environment:
 
 ```commandline
 pipenv shell
-pipenv lock && pipenv sync
+pipenv update
 pipenv install --dev
 ```
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
index fc552ac8..c8f885e3 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,164 +1,125 @@
 -i https://pypi.org/simple
-aiofiles==22.1.0
-anyio==3.6.1 ; python_full_version >= '3.6.2'
+aiofiles==23.1.0
+anyio==3.6.2 ; python_full_version >= '3.6.2'
 appdirs==1.4.4
 appnope==0.1.3 ; sys_platform == 'darwin'
-argcomplete==2.0.0 ; python_version >= '3.6'
-argh==0.26.2
-argon2-cffi==21.3.0 ; python_version >= '3.6'
-argon2-cffi-bindings==21.2.0 ; python_version >= '3.6'
-asttokens==2.0.8
-asyncpg==0.26.0
-attrs==22.1.0 ; python_version >= '3.5'
-babel==2.10.3 ; python_version >= '3.6'
+asttokens==2.2.1
+asyncpg==0.27.0
+attrs==22.2.0 ; python_version >= '3.6'
 backcall==0.2.0
-beautifulsoup4==4.11.1 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
-bleach==5.0.1 ; python_version >= '3.7'
-boto3==1.24.90
-botocore==1.27.90 ; python_version >= '3.7'
+boto3==1.26.103
+botocore==1.29.103 ; python_version >= '3.7'
 bs4==0.0.1
-canonicaljson==1.6.3 ; python_version >= '3.7'
-certifi==2022.9.24 ; python_version >= '3.6'
-cffi==1.15.1
+canonicaljson==2.0.0 ; python_version >= '3.7'
+certifi==2022.12.7 ; python_version >= '3.6'
 cfgv==3.3.1 ; python_full_version >= '3.6.1'
-charset-normalizer==2.1.1 ; python_full_version >= '3.6.0'
+charset-normalizer==3.1.0 ; python_full_version >= '3.7.0'
 click==8.1.3 ; python_version >= '3.7'
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+comm==0.1.3 ; python_version >= '3.6'
 configparser==5.3.0 ; python_version >= '3.7'
 -e .
-coverage==6.5.0
-coveralls==3.3.1
-cssselect==1.1.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-debugpy==1.6.3 ; python_version >= '3.7'
+coverage[toml]==7.2.2 ; python_version >= '3.7'
+cssselect==1.2.0 ; python_version >= '3.7'
+debugpy==1.6.6 ; python_version >= '3.7'
 decorator==5.1.1 ; python_version >= '3.5'
-defusedxml==0.7.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 distlib==0.3.6
-docopt==0.6.2
-entrypoints==0.4 ; python_version >= '3.6'
-executing==1.1.1
-fake-useragent==0.1.11
-fastapi==0.85.0
-fastjsonschema==2.16.2
-filelock==3.8.0 ; python_version >= '3.7'
-flake8==5.0.4
-flake8-annotations==2.9.1
-flake8-docstrings==1.6.0
-flake8-import-order==0.18.1
-flake8-quotes==3.3.1
-ga4gh.vrs[extras]==0.8.7.dev0 ; python_version >= '3.6'
-ga4gh.vrsatile.pydantic==0.1.dev3 ; python_version >= '3.8'
-gene-normalizer==0.2.3
-gffutils==0.11.1
+exceptiongroup==1.1.1 ; python_version < '3.11'
+executing==1.2.0
+fake-useragent==1.1.3
+fastapi==0.95.0
+filelock==3.10.7 ; python_version >= '3.7'
+flake8==6.0.0
+flake8-annotations==3.0.0
+flake8-docstrings==1.7.0
+flake8-import-order==0.18.2
+flake8-quotes==3.3.2
+ga4gh.vrs==0.9.0.dev0
+ga4gh.vrsatile.pydantic==0.1.0.dev7 ; python_version >= '3.8'
+gene-normalizer==0.2.8
 h11==0.14.0 ; python_version >= '3.7'
-hgvs==1.5.2
+hgvs==1.5.4
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-identify==2.5.6 ; python_version >= '3.7'
+identify==2.5.22 ; python_version >= '3.7'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==5.0.0 ; python_version >= '3.7'
+importlib-metadata==6.1.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
-iniconfig==1.1.1
-ipykernel==6.16.0 ; python_version >= '3.7'
-ipython==8.5.0 ; python_version >= '3.8'
-ipython-genutils==0.2.0
-jedi==0.18.1 ; python_version >= '3.6'
-jinja2==3.1.2 ; python_version >= '3.7'
+iniconfig==2.0.0 ; python_version >= '3.7'
+ipykernel==6.22.0
+ipython==8.12.0 ; python_version >= '3.8'
+jedi==0.18.2 ; python_version >= '3.6'
 jmespath==1.0.1 ; python_version >= '3.7'
-json5==0.9.10
 jsonschema==3.2.0
-jupyter-client==7.4.2 ; python_version >= '3.7'
-jupyter-core==4.11.1 ; python_version >= '3.7'
-jupyter-server==1.21.0 ; python_version >= '3.7'
-jupyterlab==3.4.8
-jupyterlab-pygments==0.2.2 ; python_version >= '3.7'
-jupyterlab-server==2.16.0 ; python_version >= '3.7'
-lxml==4.9.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.4.1 ; python_version >= '3.7'
-markupsafe==2.1.1 ; python_version >= '3.7'
+jupyter-client==8.1.0 ; python_version >= '3.8'
+jupyter-core==5.3.0 ; python_version >= '3.8'
+lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
 mccabe==0.7.0 ; python_version >= '3.6'
-mistune==2.0.4
-mock==4.0.3
-nbclassic==0.4.5 ; python_version >= '3.7'
-nbclient==0.7.0 ; python_full_version >= '3.7.0'
-nbconvert==7.2.1 ; python_version >= '3.7'
-nbformat==5.7.0 ; python_version >= '3.7'
+mock==5.0.1
 nest-asyncio==1.5.6 ; python_version >= '3.5'
 nodeenv==1.7.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6'
-notebook==6.5.1 ; python_version >= '3.7'
-notebook-shim==0.1.0 ; python_version >= '3.7'
-numpy==1.23.4 ; python_version >= '3.10'
-packaging==21.3 ; python_version >= '3.6'
-pandas==1.5.0
-pandocfilters==1.5.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+numpy==1.24.2 ; python_version >= '3.8'
+packaging==23.0 ; python_version >= '3.7'
+pandas==1.5.3
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
-platformdirs==2.5.2 ; python_version >= '3.7'
+platformdirs==3.2.0 ; python_version >= '3.7'
 pluggy==1.0.0 ; python_version >= '3.6'
-pre-commit==2.20.0
-prometheus-client==0.15.0 ; python_version >= '3.6'
-prompt-toolkit==3.0.31 ; python_full_version >= '3.6.2'
-psutil==5.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-psycopg2==2.9.4 ; python_version >= '3.6'
-psycopg2-binary==2.9.4
+pre-commit==3.2.1
+prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0'
+psutil==5.9.4 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+psycopg2==2.9.5 ; python_version >= '3.6'
+psycopg2-binary==2.9.5
 ptyprocess==0.7.0
 pure-eval==0.2.2
-py==1.11.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-pycodestyle==2.9.1 ; python_version >= '3.6'
-pycparser==2.21 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-pydantic==1.10.2
-pydocstyle==6.1.1 ; python_version >= '3.6'
+pycodestyle==2.10.0 ; python_version >= '3.6'
+pydantic==1.10.7
+pydocstyle==6.3.0 ; python_version >= '3.6'
 pyee==8.2.2
-pyfaidx==0.7.1
-pyflakes==2.5.0 ; python_version >= '3.6'
-pygments==2.13.0 ; python_version >= '3.6'
+pyflakes==3.0.1 ; python_version >= '3.6'
+pygments==2.14.0 ; python_version >= '3.6'
 pyliftover==0.4
-pyparsing==3.0.9 ; python_full_version >= '3.6.8'
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
-pyquery==1.4.3
-pyrsistent==0.18.1 ; python_version >= '3.7'
-pysam==0.19.1
-pytest==7.1.3
+pyquery==2.0.0
+pyrsistent==0.19.3 ; python_version >= '3.7'
+pysam==0.20.0
+pytest==7.2.2
 pytest-asyncio==0.18.3
 pytest-cov==4.0.0
 python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.4.1
-pytz==2022.4
+pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
-pyzmq==24.0.1 ; python_version >= '3.6'
-requests==2.28.1 ; python_version >= '3.7' and python_version < '4'
+pyzmq==25.0.2 ; python_version >= '3.6'
+requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
-send2trash==1.8.0
-setuptools==65.5.0 ; python_version >= '3.7'
-simplejson==3.17.6 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+setuptools==67.6.1 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 sniffio==1.3.0 ; python_version >= '3.7'
 snowballstemmer==2.2.0
-soupsieve==2.3.2.post1 ; python_version >= '3.6'
+soupsieve==2.4 ; python_version >= '3.7'
 sqlparse==0.4.3 ; python_version >= '3.5'
-stack-data==0.5.1
-starlette==0.20.4 ; python_version >= '3.7'
+stack-data==0.6.2
+starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
-terminado==0.16.0 ; python_version >= '3.7'
-tinycss2==1.1.1 ; python_version >= '3.6'
-toml==0.10.2 ; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
-tomli==2.0.1 ; python_version >= '3.7'
+tomli==2.0.1 ; python_version < '3.11'
 tornado==6.2 ; python_version >= '3.7'
-tqdm==4.64.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.4.0 ; python_version >= '3.7'
-typing-extensions==4.4.0 ; python_version >= '3.7'
-urllib3==1.26.12 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4'
-uvicorn==0.18.3
-virtualenv==20.16.5 ; python_version >= '3.6'
-w3lib==2.0.1 ; python_version >= '3.6'
-wcwidth==0.2.5
-webencodings==0.5.1
-websocket-client==1.4.1 ; python_version >= '3.7'
-websockets==10.3 ; python_version >= '3.7'
-yoyo-migrations==8.0.0
-zipp==3.9.0 ; python_version >= '3.7'
+tqdm==4.65.0 ; python_version >= '3.7'
+traitlets==5.9.0 ; python_version >= '3.7'
+typing-extensions==4.5.0 ; python_version >= '3.7'
+urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+uvicorn==0.21.1
+virtualenv==20.21.0 ; python_version >= '3.7'
+w3lib==2.1.1 ; python_version >= '3.7'
+wcwidth==0.2.6
+websockets==10.4 ; python_version >= '3.7'
+yoyo-migrations==8.2.0
+zipp==3.15.0 ; python_version >= '3.7'
diff --git a/requirements.txt b/requirements.txt
index f1a7b124..5eaf8560 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,92 +1,86 @@
 -i https://pypi.org/simple
-aiofiles==22.1.0
-anyio==3.6.1 ; python_full_version >= '3.6.2'
+aiofiles==23.1.0
+anyio==3.6.2 ; python_full_version >= '3.6.2'
 appdirs==1.4.4
 appnope==0.1.3 ; sys_platform == 'darwin'
-argcomplete==2.0.0 ; python_version >= '3.6'
-argh==0.26.2
-asttokens==2.0.8
-asyncpg==0.26.0
-attrs==22.1.0 ; python_version >= '3.5'
+asttokens==2.2.1
+asyncpg==0.27.0
+attrs==22.2.0 ; python_version >= '3.6'
 backcall==0.2.0
-beautifulsoup4==4.11.1 ; python_full_version >= '3.6.0'
+beautifulsoup4==4.12.0 ; python_full_version >= '3.6.0'
 biocommons.seqrepo==0.6.5
 bioutils==0.5.7 ; python_version >= '3.6'
-boto3==1.24.90
-botocore==1.27.90 ; python_version >= '3.7'
+boto3==1.26.103
+botocore==1.29.103 ; python_version >= '3.7'
 bs4==0.0.1
-canonicaljson==1.6.3 ; python_version >= '3.7'
-certifi==2022.9.24 ; python_version >= '3.6'
-charset-normalizer==2.1.1 ; python_full_version >= '3.6.0'
+canonicaljson==2.0.0 ; python_version >= '3.7'
+certifi==2022.12.7 ; python_version >= '3.6'
+charset-normalizer==3.1.0 ; python_full_version >= '3.7.0'
 click==8.1.3 ; python_version >= '3.7'
 coloredlogs==15.0.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 configparser==5.3.0 ; python_version >= '3.7'
-cssselect==1.1.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
+cssselect==1.2.0 ; python_version >= '3.7'
 decorator==5.1.1 ; python_version >= '3.5'
-executing==1.1.1
-fake-useragent==0.1.11
-fastapi==0.85.0
-ga4gh.vrs[extras]==0.8.7.dev0 ; python_version >= '3.6'
-ga4gh.vrsatile.pydantic==0.1.dev3 ; python_version >= '3.8'
-gene-normalizer==0.2.3
-gffutils==0.11.1
+executing==1.2.0
+fake-useragent==1.1.3
+fastapi==0.95.0
+ga4gh.vrs==0.9.0.dev0
+ga4gh.vrsatile.pydantic==0.1.0.dev7 ; python_version >= '3.8'
+gene-normalizer==0.2.8
 h11==0.14.0 ; python_version >= '3.7'
-hgvs==1.5.2
+hgvs==1.5.4
 humanfriendly==10.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
 idna==3.4 ; python_version >= '3.5'
-importlib-metadata==5.0.0 ; python_version >= '3.7'
+importlib-metadata==6.1.0 ; python_version >= '3.7'
 inflection==0.5.1 ; python_version >= '3.5'
-ipython==8.5.0 ; python_version >= '3.8'
-jedi==0.18.1 ; python_version >= '3.6'
+ipython==8.12.0 ; python_version >= '3.8'
+jedi==0.18.2 ; python_version >= '3.6'
 jmespath==1.0.1 ; python_version >= '3.7'
 jsonschema==3.2.0
-lxml==4.9.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
-markdown==3.4.1 ; python_version >= '3.7'
+lxml==4.9.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
+markdown==3.4.3 ; python_version >= '3.7'
 matplotlib-inline==0.1.6 ; python_version >= '3.5'
-numpy==1.23.4 ; python_version >= '3.10'
-pandas==1.5.0
+numpy==1.24.2 ; python_version >= '3.8'
+pandas==1.5.3
 parse==1.19.0
 parsley==1.3
 parso==0.8.3 ; python_version >= '3.6'
 pexpect==4.8.0 ; sys_platform != 'win32'
 pickleshare==0.7.5
-prompt-toolkit==3.0.31 ; python_full_version >= '3.6.2'
-psycopg2==2.9.4 ; python_version >= '3.6'
-psycopg2-binary==2.9.4
+prompt-toolkit==3.0.38 ; python_full_version >= '3.7.0'
+psycopg2==2.9.5 ; python_version >= '3.6'
 ptyprocess==0.7.0
 pure-eval==0.2.2
-pydantic==1.10.2
+pydantic==1.10.7
 pyee==8.2.2
-pyfaidx==0.7.1
-pygments==2.13.0 ; python_version >= '3.6'
+pygments==2.14.0 ; python_version >= '3.6'
 pyliftover==0.4
 pyppeteer==1.0.2 ; python_version >= '3.7' and python_version < '4.0'
-pyquery==1.4.3
-pyrsistent==0.18.1 ; python_version >= '3.7'
-pysam==0.19.1
+pyquery==2.0.0
+pyrsistent==0.19.3 ; python_version >= '3.7'
+pysam==0.20.0
 python-dateutil==2.8.2 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 python-jsonschema-objects==0.4.1
-pytz==2022.4
+pytz==2023.3
 pyyaml==6.0 ; python_version >= '3.6'
-requests==2.28.1 ; python_version >= '3.7' and python_version < '4'
+requests==2.28.2 ; python_version >= '3.7' and python_version < '4'
 requests-html==0.10.0 ; python_full_version >= '3.6.0'
 s3transfer==0.6.0 ; python_version >= '3.7'
-setuptools==65.5.0 ; python_version >= '3.7'
-simplejson==3.17.6 ; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
+setuptools==67.6.1 ; python_version >= '3.7'
 six==1.16.0 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
 sniffio==1.3.0 ; python_version >= '3.7'
-soupsieve==2.3.2.post1 ; python_version >= '3.6'
+soupsieve==2.4 ; python_version >= '3.7'
 sqlparse==0.4.3 ; python_version >= '3.5'
-stack-data==0.5.1
-starlette==0.20.4 ; python_version >= '3.7'
+stack-data==0.6.2
+starlette==0.26.1 ; python_version >= '3.7'
 tabulate==0.9.0 ; python_version >= '3.7'
-tqdm==4.64.1 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
-traitlets==5.4.0 ; python_version >= '3.7'
-typing-extensions==4.4.0 ; python_version >= '3.7'
-urllib3==1.26.12 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5' and python_version < '4'
-uvicorn==0.18.3
-w3lib==2.0.1 ; python_version >= '3.6'
-wcwidth==0.2.5
-websockets==10.3 ; python_version >= '3.7'
-yoyo-migrations==8.0.0
-zipp==3.9.0 ; python_version >= '3.7'
+tqdm==4.65.0 ; python_version >= '3.7'
+traitlets==5.9.0 ; python_version >= '3.7'
+typing-extensions==4.5.0 ; python_version >= '3.7'
+urllib3==1.26.15 ; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'
+uvicorn==0.21.1
+w3lib==2.1.1 ; python_version >= '3.7'
+wcwidth==0.2.6
+websockets==10.4 ; python_version >= '3.7'
+yoyo-migrations==8.2.0
+zipp==3.15.0 ; python_version >= '3.7'
diff --git a/setup.cfg b/setup.cfg
index 43fddde1..5a26ad00 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -24,12 +24,7 @@ install_requires =
     uvicorn
     fastapi
     gene-normalizer
-
-tests_require =
-    pytest
-    pytest-cov
-    pytest-asyncio == 0.18.3
-    mock
+    ga4gh.vrs
 
 [options.package_data]
 cool_seq_tool =
@@ -37,9 +32,21 @@ cool_seq_tool =
 
 [options.extras_require]
 dev =
+    pre-commit
+    flake8
+    flake8-docstrings
+    flake8-annotations
+    flake8-quotes
+    flake8-import-order
+    ipython
+    ipykernel
+    psycopg2-binary
+
+tests =
     pytest
     pytest-cov
-    psycopg2-binary
+    pytest-asyncio == 0.18.3
+    mock
 
 [tool:pytest]
 addopts = --ignore setup.py --ignore codebuild/ --doctest-modules --cov-report term-missing --disable-warnings --cov .

From 5a8c3bdd46d7a52a30fcb8b98e22b012ab97ae89 Mon Sep 17 00:00:00 2001
From: Kori Kuzma <korikuzma@gmail.com>
Date: Tue, 4 Apr 2023 05:53:26 -0700
Subject: [PATCH 4/4] refactor: remove unused instance variables (#141)

Removes `MANETranscript.hgvs_parser` and `UTADatabase.liftover_38_to_37`
---
 cool_seq_tool/data_sources/mane_transcript.py |  2 --
 cool_seq_tool/data_sources/uta_database.py    | 16 +---------------
 2 files changed, 1 insertion(+), 17 deletions(-)

diff --git a/cool_seq_tool/data_sources/mane_transcript.py b/cool_seq_tool/data_sources/mane_transcript.py
index d98b17da..62655e08 100644
--- a/cool_seq_tool/data_sources/mane_transcript.py
+++ b/cool_seq_tool/data_sources/mane_transcript.py
@@ -10,7 +10,6 @@
 import math
 from typing import Optional, Set, Tuple, Dict, List, Union
 
-import hgvs.parser
 import pandas as pd
 
 from cool_seq_tool.schemas import AnnotationLayer, Assembly, MappedManeData, \
@@ -47,7 +46,6 @@ def __init__(self, seqrepo_access: SeqRepoAccess,
         :param GeneNormalizer gene_normalizer: Access to Gene Normalizer
         """
         self.seqrepo_access = seqrepo_access
-        self.hgvs_parser = hgvs.parser.Parser()
         self.transcript_mappings = transcript_mappings
         self.mane_transcript_mappings = mane_transcript_mappings
         self.uta_db = uta_db
diff --git a/cool_seq_tool/data_sources/uta_database.py b/cool_seq_tool/data_sources/uta_database.py
index 089b0a3e..a4b1c7b9 100644
--- a/cool_seq_tool/data_sources/uta_database.py
+++ b/cool_seq_tool/data_sources/uta_database.py
@@ -23,7 +23,6 @@
 
 # Environment variables for paths to chain files for pyliftover
 LIFTOVER_CHAIN_37_TO_38 = environ.get("LIFTOVER_CHAIN_37_TO_38")
-LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
 
 
 class UTADatabase:
@@ -33,8 +32,7 @@ def __init__(
         self,
         db_url: str = UTA_DB_URL,
         db_pwd: str = "",
-        chain_file_37_to_38: Optional[str] = None,
-        chain_file_38_to_37: Optional[str] = None
+        chain_file_37_to_38: Optional[str] = None
     ) -> None:
         """Initialize DB class. Downstream libraries should use the create()
         method to construct a new instance: await UTADatabase.create()
@@ -46,10 +44,6 @@ def __init__(
             This is used for pyliftover. If this is not provided, will check to see if
             LIFTOVER_CHAIN_37_TO_38 env var is set. If neither is provided, will allow
             pyliftover to download a chain file from UCSC
-        :param chain_file_38_to_37: Optional path to chain file for 38 to 37 assembly.
-            This is used for pyliftover. If this is not provided, will check to see if
-            LIFTOVER_CHAIN_38_TO_37 env var is set. If neither is provided, will allow
-            pyliftover to download a chain file from UCSC
         """
         self.schema = None
         self.db_url = db_url
@@ -63,12 +57,6 @@ def __init__(
         else:
             self.liftover_37_to_38 = LiftOver("hg19", "hg38")
 
-        chain_file_38_to_37 = chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37
-        if chain_file_38_to_37:
-            self.liftover_38_to_37 = LiftOver(chain_file_38_to_37)
-        else:
-            self.liftover_38_to_37 = LiftOver("hg38", "hg19")
-
     @staticmethod
     def _update_db_url(db_pwd: str, db_url: str) -> str:
         """Return new db_url containing password.
@@ -1022,8 +1010,6 @@ def get_liftover(self, chromosome: str, pos: int,
 
         if liftover_to_assembly == Assembly.GRCH38:
             liftover = self.liftover_37_to_38.convert_coordinate(chromosome, pos)
-        elif liftover_to_assembly == Assembly.GRCH37:
-            liftover = self.liftover_38_to_37.convert_coordinate(chromosome, pos)
         else:
             logger.warning(f"{liftover_to_assembly} assembly not supported")
             liftover = None