feat!: add chromosome lookup to sequence reference utils (#67)

I just realized that you need to also know the chromosome name for your refget accession ID to do liftover, so I just moved stuff around in that module so both assembly and chromosome are returned.

Author: jsstevenson

src/agct/__init__.py

@@ -1,13 +1,18 @@
 """Provide fast liftover in Python via the ``chainfile`` crate."""
 
-from agct.assembly_registry import Assembly, get_assembly_from_refget_id
 from agct.converter import Converter, LiftoverResult, Strand, get_converter
+from agct.seqref_registry import (
+    Assembly,
+    get_refget_id_from_seqinfo,
+    get_seqinfo_from_refget_id,
+)
 
 __all__ = [
     "Assembly",
     "Converter",
     "LiftoverResult",
     "Strand",
-    "get_assembly_from_refget_id",
     "get_converter",
+    "get_refget_id_from_seqinfo",
+    "get_seqinfo_from_refget_id",
 ]

src/agct/assembly_registry.py

@@ -12,7 +12,7 @@
 from wags_tails.utils.storage import get_data_dir
 
 import agct._core as _core
-from agct.assembly_registry import Assembly
+from agct.seqref_registry import Assembly
 
 _logger = logging.getLogger(__name__)
 
@@ -73,7 +73,7 @@ def __init__(
             try:
                 file_prefix = f"chainfile_{from_assembly.value}_to_{to_assembly.value}"
             except AttributeError as e:
-                msg = f"Assembly args must be instance of `agct.assembly_registry.Genome`, instead got from_assembly={from_assembly} and to_assembly={to_assembly}"
+                msg = f"Assembly args must be instance of `agct.seqref_registry.Genome`, instead got from_assembly={from_assembly} and to_assembly={to_assembly}"
                 _logger.exception(msg)
                 raise ValueError(msg) from e
 

src/agct/converter.py

@@ -0,0 +1,152 @@
+"""Sequence reference registry.
+
+Maps refget accessions (``SQ.*``) to a tuple of (:class:`Assembly`, :class:`Chromosome`)
+and exposes helpers to look up the assembly/chromosome for a given ID. The registry is
+curated for internally-used builds (currently ``hg19``/``hg38``); extend as needed.
+"""
+
+import logging
+import re
+from enum import StrEnum
+
+_logger = logging.getLogger(__name__)
+
+
+class Assembly(StrEnum):
+    """Constrain reference genome assembly values.
+
+    We could conceivably support every UCSC chainfile offering, but for now, we'll
+    stick with internal use cases only.
+    """
+
+    HG38 = "hg38"
+    HG19 = "hg19"
+
+
+class Chromosome(StrEnum):
+    """Constrain chromosome values to UCSC-style names.
+
+    This class should NOT be used to type-constrain input in the converter
+    module, because in practice, chainfiles can use any name for an accession. In practice,
+    though, we're mostly interested in UCSC chainfiles, so this class is provided as a
+    utility for likely-relevant chromosome names.
+    """
+
+    CHR1 = "chr1"
+    CHR2 = "chr2"
+    CHR3 = "chr3"
+    CHR4 = "chr4"
+    CHR5 = "chr5"
+    CHR6 = "chr6"
+    CHR7 = "chr7"
+    CHR8 = "chr8"
+    CHR9 = "chr9"
+    CHR10 = "chr10"
+    CHR11 = "chr11"
+    CHR12 = "chr12"
+    CHR13 = "chr13"
+    CHR14 = "chr14"
+    CHR15 = "chr15"
+    CHR16 = "chr16"
+    CHR17 = "chr17"
+    CHR18 = "chr18"
+    CHR19 = "chr19"
+    CHR20 = "chr20"
+    CHR21 = "chr21"
+    CHR22 = "chr22"
+    CHRX = "chrX"
+    CHRY = "chrY"
+
+
+REFGET_ID_INFO = {
+    "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO": (Assembly.HG38, Chromosome.CHR1),
+    "SQ.pnAqCRBrTsUoBghSD1yp_jXWSmlbdh4g": (Assembly.HG38, Chromosome.CHR2),
+    "SQ.Zu7h9AggXxhTaGVsy7h_EZSChSZGcmgX": (Assembly.HG38, Chromosome.CHR3),
+    "SQ.HxuclGHh0XCDuF8x6yQrpHUBL7ZntAHc": (Assembly.HG38, Chromosome.CHR4),
+    "SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI": (Assembly.HG38, Chromosome.CHR5),
+    "SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV": (Assembly.HG38, Chromosome.CHR6),
+    "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul": (Assembly.HG38, Chromosome.CHR7),
+    "SQ.209Z7zJ-mFypBEWLk4rNC6S_OxY5p7bs": (Assembly.HG38, Chromosome.CHR8),
+    "SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI": (Assembly.HG38, Chromosome.CHR9),
+    "SQ.ss8r_wB0-b9r44TQTMmVTI92884QvBiB": (Assembly.HG38, Chromosome.CHR10),
+    "SQ.2NkFm8HK88MqeNkCgj78KidCAXgnsfV1": (Assembly.HG38, Chromosome.CHR11),
+    "SQ.6wlJpONE3oNb4D69ULmEXhqyDZ4vwNfl": (Assembly.HG38, Chromosome.CHR12),
+    "SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT": (Assembly.HG38, Chromosome.CHR13),
+    "SQ.eK4D2MosgK_ivBkgi6FVPg5UXs1bYESm": (Assembly.HG38, Chromosome.CHR14),
+    "SQ.AsXvWL1-2i5U_buw6_niVIxD6zTbAuS6": (Assembly.HG38, Chromosome.CHR15),
+    "SQ.yC_0RBj3fgBlvgyAuycbzdubtLxq-rE0": (Assembly.HG38, Chromosome.CHR16),
+    "SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7": (Assembly.HG38, Chromosome.CHR17),
+    "SQ.vWwFhJ5lQDMhh-czg06YtlWqu0lvFAZV": (Assembly.HG38, Chromosome.CHR18),
+    "SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl": (Assembly.HG38, Chromosome.CHR19),
+    "SQ.-A1QmD_MatoqxvgVxBLZTONHz9-c7nQo": (Assembly.HG38, Chromosome.CHR20),
+    "SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8": (Assembly.HG38, Chromosome.CHR21),
+    "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ": (Assembly.HG38, Chromosome.CHR22),
+    "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP": (Assembly.HG38, Chromosome.CHRX),
+    "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5": (Assembly.HG38, Chromosome.CHRY),
+    "SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU": (Assembly.HG19, Chromosome.CHR1),
+    "SQ.9KdcA9ZpY1Cpvxvg8bMSLYDUpsX6GDLO": (Assembly.HG19, Chromosome.CHR2),
+    "SQ.VNBualIltAyi2AI_uXcKU7M9XUOuA7MS": (Assembly.HG19, Chromosome.CHR3),
+    "SQ.iy7Zfceb5_VGtTQzJ-v5JpPbpeifHD_V": (Assembly.HG19, Chromosome.CHR4),
+    "SQ.vbjOdMfHJvTjK_nqvFvpaSKhZillW0SX": (Assembly.HG19, Chromosome.CHR5),
+    "SQ.KqaUhJMW3CDjhoVtBetdEKT1n6hM-7Ek": (Assembly.HG19, Chromosome.CHR6),
+    "SQ.IW78mgV5Cqf6M24hy52hPjyyo5tCCd86": (Assembly.HG19, Chromosome.CHR7),
+    "SQ.tTm7wmhz0G4lpt8wPspcNkAD_qiminj6": (Assembly.HG19, Chromosome.CHR8),
+    "SQ.HBckYGQ4wYG9APHLpjoQ9UUe9v7NxExt": (Assembly.HG19, Chromosome.CHR9),
+    "SQ.-BOZ8Esn8J88qDwNiSEwUr5425UXdiGX": (Assembly.HG19, Chromosome.CHR10),
+    "SQ.XXi2_O1ly-CCOi3HP5TypAw7LtC6niFG": (Assembly.HG19, Chromosome.CHR11),
+    "SQ.105bBysLoDFQHhajooTAUyUkNiZ8LJEH": (Assembly.HG19, Chromosome.CHR12),
+    "SQ.Ewb9qlgTqN6e_XQiRVYpoUfZJHXeiUfH": (Assembly.HG19, Chromosome.CHR13),
+    "SQ.5Ji6FGEKfejK1U6BMScqrdKJK8GqmIGf": (Assembly.HG19, Chromosome.CHR14),
+    "SQ.zIMZb3Ft7RdWa5XYq0PxIlezLY2ccCgt": (Assembly.HG19, Chromosome.CHR15),
+    "SQ.W6wLoIFOn4G7cjopxPxYNk2lcEqhLQFb": (Assembly.HG19, Chromosome.CHR16),
+    "SQ.AjWXsI7AkTK35XW9pgd3UbjpC3MAevlz": (Assembly.HG19, Chromosome.CHR17),
+    "SQ.BTj4BDaaHYoPhD3oY2GdwC_l0uqZ92UD": (Assembly.HG19, Chromosome.CHR18),
+    "SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX": (Assembly.HG19, Chromosome.CHR19),
+    "SQ.iy_UbUrvECxFRX5LPTH_KPojdlT7BKsf": (Assembly.HG19, Chromosome.CHR20),
+    "SQ.LpTaNW-hwuY_yARP0rtarCnpCQLkgVCg": (Assembly.HG19, Chromosome.CHR21),
+    "SQ.XOgHwwR3Upfp5sZYk6ZKzvV25a4RBVu8": (Assembly.HG19, Chromosome.CHR22),
+    "SQ.v7noePfnNpK8ghYXEqZ9NukMXW7YeNsm": (Assembly.HG19, Chromosome.CHRX),
+    "SQ.BT7QyW5iXaX_1PSX-msSGYsqRdMKqkj-": (Assembly.HG19, Chromosome.CHRY),
+}
+
+REFGET_ID_LOOKUP = {v: k for k, v in REFGET_ID_INFO.items()}
+
+
+_REFGET_AC_PATTERN = re.compile(r"^SQ\.[0-9A-Za-z_\\-]{32}$")
+
+
+def get_seqinfo_from_refget_id(
+    refget_accession: str,
+) -> tuple[Assembly, Chromosome] | None:
+    """Given a GA4GH SequenceReference refget accession ID, get back its reference genome and chromosome name
+
+    .. code-block:: pycon
+
+        >>> from agct.assembly_registry import get_assembly_from_refget_id
+        >>> get_assembly_from_refget_id("SQ.pnAqCRBrTsUoBghSD1yp_jXWSmlbdh4g")
+        (<Assembly.HG38: 'hg38'>, <Chromosome.CHR2: 'chr2'>)
+
+    Use for acquiring a converter instance and calling liftover on a referenced GA4GH
+    variation object.
+
+    :param refget_accession: sequence reference (must start with `"SQ."`)
+    :return: a reference assembly and chromosome, if successful
+    :raise ValueError: if input appears to be in an invalid format for a refget accession ID
+    """
+    if not re.match(_REFGET_AC_PATTERN, refget_accession):
+        msg = f"refget accession ID must be in format 'SQ.ABCDEFGHIJKLMNOPQRSTUVWXYZ123456'; got {refget_accession}"
+        _logger.error(msg)
+        raise ValueError(msg)
+    return REFGET_ID_INFO.get(refget_accession)
+
+
+def get_refget_id_from_seqinfo(
+    assembly: Assembly, chromosome: Chromosome
+) -> str | None:
+    """Given an assembly/chromosome pairing, get a refget accession ID, if known
+
+    :param assembly: reference assembly for sequence
+    :param chromosome: chromosome name
+    :return: a refget sequence accession ID, if known
+    """
+    return REFGET_ID_LOOKUP.get((assembly, chromosome))