cool-seq-tool 0.4.0.dev3__py3-none-any.whl → 0.5.0__py3-none-any.whl

cool_seq_tool/mappers/liftover.py

@@ -0,0 +1,90 @@
+"""Module for mapping to/from human genome assemblies.
+
+Currently only supports GRCh37 <-> GRCh38
+"""
+
+import logging
+from os import environ
+
+from agct import Converter, Genome
+
+from cool_seq_tool.schemas import Assembly
+from cool_seq_tool.utils import process_chromosome_input
+
+# Environment variables for paths to chain files for agct
+LIFTOVER_CHAIN_37_TO_38 = environ.get("LIFTOVER_CHAIN_37_TO_38")
+LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
+
+
+_logger = logging.getLogger(__name__)
+
+
+class LiftOver:
+    """Class for mapping to/from human genome assemblies
+
+    Currently only supports GRCh37 <-> GRCh38
+    """
+
+    def __init__(
+        self,
+        chain_file_37_to_38: str | None = None,
+        chain_file_38_to_37: str | None = None,
+    ) -> None:
+        """Initialize liftover class
+
+        :param chain_file_37_to_38: Optional path to chain file for 37 to 38 assembly.
+            This is used for ``agct``. 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 ``agct`` 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 ``agct``. 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 ``agct`` to download a chain file from UCSC
+        """
+        self.from_37_to_38 = Converter(
+            chainfile=chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38,
+            from_db=Genome.HG19,
+            to_db=Genome.HG38,
+        )
+        self.from_38_to_37 = Converter(
+            chainfile=chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37,
+            from_db=Genome.HG38,
+            to_db=Genome.HG19,
+        )
+
+    def get_liftover(
+        self, chromosome: str, pos: int, liftover_to_assembly: Assembly
+    ) -> tuple[str, int] | None:
+        """Get new genome assembly data for a position on a chromosome.
+
+        Use a UCSC-style chromosome name:
+
+        >>> from cool_seq_tool.mappers import LiftOver
+        >>> from cool_seq_tool.schemas import Assembly
+        >>> lo = LiftOver()
+        >>> lo.get_liftover("chr7", 140453136, Assembly.GRCH38)
+        ('chr7', 140753336)
+
+        Chromosome names can also be NCBI-style, without prefixes:
+
+        >>> lo.get_liftover("7", 140453136, Assembly.GRCH38)
+        ('chr7', 140753336)
+
+        :param chromosome: The chromosome number, e.g. ``"chr7"``, ``"chrX"``, ``"5"``.
+        :param pos: Position on the chromosome
+        :param liftover_to_assembly: Assembly to liftover to
+        :return: Target chromosome and target position for assembly
+        """
+        chromosome = process_chromosome_input(chromosome, "LiftOver.get_liftover()")
+        if liftover_to_assembly == Assembly.GRCH38:
+            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos)
+        elif liftover_to_assembly == Assembly.GRCH37:
+            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos)
+        else:
+            _logger.warning("%s assembly not supported", liftover_to_assembly)
+            liftover = None
+
+        if not liftover:
+            _logger.warning("%s does not exist on %s", pos, chromosome)
+            return None
+        return liftover[0][:2]