refactor: add back UTADatabase.liftover_38_to_37 (#143)

GenomicMedLab · Apr 4, 2023 · 7d78e6c · 7d78e6c
1 parent c8126d9
commit 7d78e6c
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Showing 2 changed files with 16 additions and 2 deletions.
diff --git a/cool_seq_tool/data_sources/uta_database.py b/cool_seq_tool/data_sources/uta_database.py
@@ -23,6 +23,7 @@
 
 # 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:
@@ -32,7 +33,8 @@ def __init__(
         self,
         db_url: str = UTA_DB_URL,
         db_pwd: str = "",
-        chain_file_37_to_38: Optional[str] = None
+        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()
@@ -44,6 +46,10 @@ 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
@@ -57,6 +63,12 @@ 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.
@@ -1010,6 +1022,8 @@ 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

diff --git a/cool_seq_tool/version.py b/cool_seq_tool/version.py
@@ -1 +1 @@
-__version__ = "0.1.10"
+__version__ = "0.1.11"