consenrich 0.7.5b1__cp314-cp314-macosx_10_15_x86_64.whl

consenrich/constants.py

@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+r"""Various constants and genome resources used in Consenrich."""
+
+import logging
+import os
+from typing import List, Optional
+
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s - %(module)s.%(funcName)s -  %(levelname)s - %(message)s",
+)
+logging.basicConfig(
+    level=logging.WARNING,
+    format="%(asctime)s - %(module)s.%(funcName)s -  %(levelname)s - %(message)s",
+)
+logger = logging.getLogger(__name__)
+
+EFFECTIVE_GENOME_SIZES = {
+    "hg19": {
+        50: 2685511454,
+        75: 2736124898,
+        100: 2776919708,
+        150: 2827436883,
+        200: 2855463800,
+        250: 2855044784,
+    },
+    "hg38": {
+        50: 2701495711,
+        75: 2747877702,
+        100: 2805636231,
+        150: 2862010428,
+        200: 2887553103,
+        250: 2898802627,
+    },
+    "t2t": {
+        50: 2725240337,
+        75: 2786136059,
+        100: 2814334875,
+        150: 2931551487,
+        200: 2936403235,
+        250: 2960856300,
+    },
+    "mm10": {
+        50: 2308125299,
+        75: 2407883243,
+        100: 2467481008,
+        150: 2494787038,
+        200: 2520868989,
+        250: 2538590322,
+    },
+    "mm39": {
+        50: 2309746861,
+        75: 2410055689,
+        100: 2468088461,
+        150: 2495461690,
+        200: 2521902382,
+        250: 2538633971,
+    },
+    "dm3": {
+        50: 130428510,
+        75: 135004387,
+        100: 139647132,
+        150: 144307658,
+        200: 148523810,
+        250: 151901455,
+    },
+    "dm6": {
+        50: 125464678,
+        75: 127324557,
+        100: 129789773,
+        150: 129940985,
+        200: 132508963,
+        250: 132900923,
+    },
+    "ce11": {
+        50: 95159402,
+        75: 96945370,
+        100: 98259898,
+        150: 98721103,
+        200: 98672558,
+        250: 101271756,
+    },
+}
+
+
+def resolveGenomeName(genome: str) -> str:
+    r"""Standardize the genome name for consistency
+    :param genome: Name of the genome. See :class:`consenrich.core.genomeParams`.
+    :type genome: str
+    :return: Standardized genome name.
+    :rtype: str
+    :raises ValueError: If the genome is not recognized.
+    """
+    genome_ = genome.lower()
+    if genome_ in ["hg19", "grch37"]:
+        return "hg19"
+    elif genome_ in ["hg38", "grch38"]:
+        return "hg38"
+    elif genome_ in ["t2t", "chm13", "t2t-chm13"]:
+        return "t2t"
+    elif genome_ in ["mm10", "grcm38"]:
+        return "mm10"
+    elif genome_ in ["mm39", "grcm39"]:
+        return "mm39"
+    elif genome_ in ["dm3"]:
+        return "dm3"
+    elif genome_ in ["dm6"]:
+        return "dm6"
+    elif genome_ in ["ce10", "ws220"]:
+        return "ce10"
+    elif genome_ in ["ce11", "wbcel235"]:
+        return "ce11"
+    raise ValueError(
+        f"Genome {genome} is not recognized. Please provide a valid genome name or manually specify resources"
+    )
+
+
+def getEffectiveGenomeSize(genome: str, readLength: int) -> int:
+    r"""Get the effective genome size for a given genome and read length.
+
+    :param genome: Name of the genome. See :func:`consenrich.constants.resolveGenomeName` and :class:`consenrich.core.genomeParams`.
+    :type genome: str
+    :param readLength: Length of the reads. See :func:`consenrich.core.getReadLength`.
+    :type readLength: int
+    :raises ValueError: If the genome is not recognized or if the read length is not available for the genome.
+    :return: Effective genome size in base pairs.
+    :rtype: int
+    """
+
+    global EFFECTIVE_GENOME_SIZES
+    genome_: str = resolveGenomeName(genome)
+    if genome_ in EFFECTIVE_GENOME_SIZES:
+        if readLength not in EFFECTIVE_GENOME_SIZES[genome_]:
+            nearestReadLength: int = int(
+                min(
+                    EFFECTIVE_GENOME_SIZES[genome_].keys(),
+                    key=lambda x: abs(x - readLength),
+                )
+            )
+            return EFFECTIVE_GENOME_SIZES[genome_][nearestReadLength]
+        return EFFECTIVE_GENOME_SIZES[genome_][readLength]
+    raise ValueError(f"Defaults not available for {genome}")
+
+
+def getGenomeResourceFile(
+    genome: str, fileType: str, dir_: str = "data"
+):
+    r"""Get the path to a genome resource file.
+
+    :param genome: the genome assembly. See :func:`consenrich.constants.resolveGenomeName` and :class:`consenrich.core.genomeParams`.
+    :type genome: str
+    :param fileType: One of 'sizes', 'blacklist', 'sparse'.
+    :type fileType: str
+    :return: Path to the resource file.
+    :rtype: str
+    :raises ValueError: If not a sizes, blacklist, or sparse file.
+    :raises FileNotFoundError: If the resource file does not exist.
+    """
+    if fileType.lower() in ["sizes"]:
+        fileName = f"{genome}.sizes"
+    elif fileType.lower() in ["blacklist"]:
+        fileName = f"{genome}_blacklist.bed"
+    elif fileType.lower() in ["sparse"]:
+        fileName = f"{genome}_sparse.bed"
+    filePath = os.path.join(
+        os.path.dirname(__file__), os.path.join(dir_, fileName)
+    )
+    if not os.path.exists(filePath):
+        raise FileNotFoundError(
+            f"Resource file {filePath} does not exist."
+        )
+    return filePath