consenrich 0.7.5b1__cp314-cp314-macosx_10_15_x86_64.whl

consenrich/misc_util.py

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+# -*- coding: utf-8 -*-
+r"""
+==============================================================================
+`consenrich.misc_util` -- Miscellaneous utility functions
+==============================================================================
+
+"""
+
+import os
+from typing import List, Optional, Tuple
+import logging
+import re
+import numpy as np
+import pandas as pd
+import pybedtools as bed
+import pysam as sam
+
+from scipy import signal, ndimage
+
+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__)
+
+
+def checkBamFile(bamFile: str) -> bool:
+    r"""Check that the bam file exists and is indexed
+
+    Assumes the bam file is sorted by coordinates
+    """
+    has_index = False
+    if not os.path.exists(bamFile):
+        raise FileNotFoundError(f"Could not find {bamFile}")
+    try:
+        bamfile = sam.AlignmentFile(bamFile, "rb")
+        has_index = bamfile.check_index()
+        bamfile.close()
+    except AttributeError as aex:
+        logger.info(f"Alignments must be in BAM format:\n{aex}")
+        raise
+    except ValueError as vex:
+        has_index = False
+        pass
+
+    if not has_index:
+        try:
+            logger.info(
+                f"Could not find index file for {bamFile}. Calling pysam.index()"
+            )
+            sam.index(bamFile)
+            has_index = True
+        except Exception as ex:
+            logger.warning(
+                f"Encountered the following exception\n{ex}\nCould not create index file for {bamFile}: is it sorted?"
+            )
+
+    return has_index
+
+
+def bamsArePairedEnd(
+    bamFiles: List[str], maxReads: int = 1_000
+) -> List[bool]:
+    """
+    Take a list of BAM files, return a list (bool) indicating whether
+    each BAM contains paired-end reads (True) or only single-end reads (False).
+
+    :param bamFiles: List of paths to BAM files
+    :type bamFiles: List[str]
+    :param maxReads: Maximum number of reads to check in each BAM file
+    :type maxReads: int
+    :return: List of booleans corresponding to each BAM file
+    :rtype: List[bool]
+    """
+
+    results = []
+    for path in bamFiles:
+        paired = False
+        seen = 0
+        with sam.AlignmentFile(path, "rb") as bam:
+            for rec in bam.fetch(until_eof=True):
+                if rec.is_paired:
+                    paired = True
+                    break
+                seen += 1
+                if maxReads is not None and seen >= maxReads:
+                    break
+        results.append(paired)
+    return results
+
+
+def getChromSizesDict(
+    sizes_file: str,
+    excludeRegex: str = r"^chr[A-Za-z0-9]+$",
+    excludeChroms: Optional[List[str]] = None,
+) -> dict:
+    r"""The function getChromSizesDict is a helper to get chromosome sizes file as a dictionary.
+    :param sizes_file: Path to a genome assembly's chromosome sizes file
+    :param exclude_regex: Regular expression to exclude chromosomes. Default: all non-standard chromosomes.
+    :param exclude_chroms: List of chromosomes to exclude.
+    :return: Dictionary of chromosome sizes. Formatted as `{chromosome_name: size}`
+    """
+    if excludeChroms is None:
+        excludeChroms = []
+    return {
+        k: v
+        for k, v in pd.read_csv(
+            sizes_file,
+            sep="\t",
+            header=None,
+            index_col=0,
+            names=["chrom", "size"],
+        )["size"]
+        .to_dict()
+        .items()
+        if re.search(excludeRegex, k) is not None
+        and k not in excludeChroms
+    }

consenrich-0.7.5b1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: consenrich
+Version: 0.7.5b1
+Summary: Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets
+Author-email: "Nolan H. Hamilton" <nolan.hamilton@unc.edu>
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cython>=3.0
+Requires-Dist: numpy>=2.1
+Requires-Dist: scipy>=1.15
+Requires-Dist: pandas>=2.3.0
+Requires-Dist: pysam>=0.23.3
+Requires-Dist: pybedtools>=0.11.2
+Requires-Dist: PyYAML>=6.0.2
+Requires-Dist: PyWavelets>=1.9.0
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.3; extra == "docs"
+Requires-Dist: sphinx-press-theme; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: myst-parser>=2.0; extra == "docs"
+Requires-Dist: sphinx-autodoc-typehints>=2.1; extra == "docs"
+Requires-Dist: sphinx-autobuild>=2025.2; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex>=2.4.0; extra == "docs"
+Dynamic: license-file
+Dynamic: requires-python
+
+# Consenrich
+
+Consenrich is an adaptive linear state estimator that yields genome-wide, uncertainty-calibrated signal tracks from noisy multi-sample cohorts' epigenetic HTS data.
+
+<p align="center">
+  <img src="docs/images/noise.png" alt="Simplified Schematic of Consenrich." width="600">
+</p>
+
+
+Special emphasis is placed on computational efficiency, model interpretability, and practical utility for downstream tasks that require well-resolved genome-wide signal estimates and uncertainty quantification across samples, such as:
+
+* Consensus detection of open chromatin regions, TF binding, histone modification, etc.
+* Candidate prioritization for differential analyses, functional validation, integrative modeling, etc.
+
+[**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/) for usage examples, installation details, configuration options, and an API reference.
+
+
+## Manuscript Preprint and Citation
+
+**BibTeX Citation**
+
+```bibtex
+@article {Hamilton2025,
+	author = {Hamilton, Nolan H and Huang, Yu-Chen E and McMichael, Benjamin D and Love, Michael I and Furey, Terrence S},
+	title = {Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data},
+	year = {2025},
+	doi = {10.1101/2025.02.05.636702},
+	publisher = {Cold Spring Harbor Laboratory},
+	journal = {bioRxiv}
+}
+```

consenrich-0.7.5b1.dist-info/RECORD

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+consenrich-0.7.5b1.dist-info/RECORD,,
+consenrich-0.7.5b1.dist-info/WHEEL,sha256=4Cxp45cRJjM_RhSwJ40gZB-W75KdWWT7Z-2loeADFVA,138
+consenrich-0.7.5b1.dist-info/entry_points.txt,sha256=EXIGcSTyc16vtPkfHJNs-aaSVoq6Pn5Ev5GeW1JCYn0,58
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+consenrich-0.7.5b1.dist-info/METADATA,sha256=SxSlHRYn_K7ri9AbCrHX2mVuVi7xJwmAbfGPzd0eQZE,2559
+consenrich-0.7.5b1.dist-info/licenses/LICENSE,sha256=w09-aT0LFrH_cL3ShJWz-xusRpbThwTpdmBD08tc8EI,1074

consenrich-0.7.5b1.dist-info/WHEEL

@@ -0,0 +1,6 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: false
+Tag: cp314-cp314-macosx_10_15_x86_64
+Generator: delocate 0.13.0
+

consenrich-0.7.5b1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+consenrich = consenrich.consenrich:main

consenrich-0.7.5b1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Nolan H. Hamilton
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

consenrich-0.7.5b1.dist-info/top_level.txt

@@ -0,0 +1 @@
+consenrich