telometer 2.0.1__tar.gz → 2.0.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- telometer-2.0.2/LICENSE.txt +19 -0
- telometer-2.0.2/PKG-INFO +48 -0
- telometer-2.0.2/pyproject.toml +55 -0
- telometer-2.0.2/telometer/__init__.py +3 -0
- {telometer-2.0.1 → telometer-2.0.2}/telometer/telometer.py +29 -14
- {telometer-2.0.1 → telometer-2.0.2}/telometer/variant_support_v2.py +1 -1
- telometer-2.0.2/telometer.egg-info/PKG-INFO +48 -0
- {telometer-2.0.1 → telometer-2.0.2}/telometer.egg-info/SOURCES.txt +3 -0
- telometer-2.0.2/telometer.egg-info/entry_points.txt +2 -0
- telometer-2.0.2/telometer.egg-info/requires.txt +5 -0
- telometer-2.0.1/PKG-INFO +0 -16
- telometer-2.0.1/pyproject.toml +0 -31
- telometer-2.0.1/telometer.egg-info/PKG-INFO +0 -16
- telometer-2.0.1/telometer.egg-info/requires.txt +0 -2
- {telometer-2.0.1 → telometer-2.0.2}/README.md +0 -0
- {telometer-2.0.1 → telometer-2.0.2}/setup.cfg +0 -0
- {telometer-2.0.1 → telometer-2.0.2}/telometer/telometer_variant_support.py +0 -0
- {telometer-2.0.1 → telometer-2.0.2}/telometer.egg-info/dependency_links.txt +0 -0
- {telometer-2.0.1 → telometer-2.0.2}/telometer.egg-info/top_level.txt +0 -0
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Copyright (c) 2024 The Python Packaging Authority
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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telometer-2.0.2/PKG-INFO
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Metadata-Version: 2.2
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Name: telometer
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Version: 2.0.2
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Summary: Quantitative digital telomere measurement from nanopore long reads
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Author-email: "Santiago E. Sanchez" <santy.esanchez@gmail.com>
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License: Copyright (c) 2024 The Python Packaging Authority
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Classifier: Development Status :: 4 - Beta
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Requires-Python: >=3.8
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Description-Content-Type: text/markdown
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License-File: LICENSE.txt
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Requires-Dist: numpy
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Requires-Dist: pandas
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Requires-Dist: pysam
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Requires-Dist: regex
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Requires-Dist: scipy
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A simple tool for measuring chromosome-specific telomeres from long-read alignments.
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[Telometer Github](https://github.com/santiago-es/Telometer)
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[build-system]
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requires = [
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"setuptools>=61,<76",
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"wheel"
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]
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build-backend = "setuptools.build_meta"
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[project]
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name = "telometer"
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version = "2.0.2"
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description = "Quantitative digital telomere measurement from nanopore long reads"
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readme = { file = "README.md", content-type = "text/markdown" }
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requires-python = ">=3.8"
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license = { file = "LICENSE.txt" }
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authors = [
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{ name = "Santiago E. Sanchez", email = "santy.esanchez@gmail.com" }
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]
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classifiers = [
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"Development Status :: 4 - Beta",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: Bio-Informatics"
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]
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dependencies = [
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"numpy",
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"pandas",
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"pysam",
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"regex",
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"scipy"
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]
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[project.scripts]
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telometer = "telometer.telometer:run_telometer"
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[tool.setuptools]
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["."]
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include = ["telometer", "telometer.*"]
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exclude = ["build", "build.*", "dist", "dist.*"]
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#!/usr/bin/env python3
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# Telometer v2.0
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# Telometer v2.0
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# Created by: Santiago E Sanchez
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# Artandi Lab, Stanford University, 2024
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# Measures telomeres from ONT long reads
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# Simple Usage: telometer -b sorted_t2t.bam -o output.tsv
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# Optional enrichment: add -e to your existing Telometer command.
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# -e adds the sample-level telomeres_per_gb column and console totals. Each QNAME
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# contributes one consistent recorded full length, including soft/hard clips,
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# before any Telometer filter. Missing/conflicting lengths yield NA, not a
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# partial-denominator rate. This measures yield represented by the input BAM;
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# reads/bases removed upstream without retained metadata cannot be recovered.
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# Memory for -e scales with unique read IDs; -l is not a total-RSS limit.
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__version__ = "2.0"
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__version__ = "2.0.2"
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import pysam
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from pathlib import Path
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from variant_support_v2 import (BASE_COLUMNS, VARIANT_COLUMNS, TRACT_COLUMNS,
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validate_variant_options, strict_runs, coverage_prefix, combined_window_density, summarize_variant)
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#from variant_support_v2 import (BASE_COLUMNS, VARIANT_COLUMNS, TRACT_COLUMNS,
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# validate_variant_options, strict_runs, coverage_prefix, combined_window_density, summarize_variant)
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import regex as re
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import pandas as pd
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import time
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from multiprocessing import Pool, cpu_count
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import numpy as np
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from scipy.signal import savgol_filter
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from telometer_variant_support import alignment_fields, cached_findall, note, reverse_complement_iupac, stable_record_key
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#from telometer_variant_support import alignment_fields, cached_findall, note, reverse_complement_iupac, stable_record_key
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from .variant_support_v2 import (
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BASE_COLUMNS,
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VARIANT_COLUMNS,
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TRACT_COLUMNS,
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validate_variant_options,
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strict_runs,
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coverage_prefix,
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combined_window_density,
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summarize_variant,
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)
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from .telometer_variant_support import (
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alignment_fields,
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cached_findall,
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note,
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reverse_complement_iupac,
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stable_record_key,
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)
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def reverse_complement(seq):
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complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N'}
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from telometer_variant_support import reverse_complement_iupac
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from .telometer_variant_support import reverse_complement_iupac
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BASE_COLUMNS = ['chromosome', 'reference_start', 'reference_end', 'telomere_length',
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'read_id', 'mapping_quality', 'read_length', 'arm', 'direction']
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Metadata-Version: 2.2
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Name: telometer
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Version: 2.0.2
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Summary: Quantitative digital telomere measurement from nanopore long reads
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Author-email: "Santiago E. Sanchez" <santy.esanchez@gmail.com>
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License: Copyright (c) 2024 The Python Packaging Authority
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Classifier: Development Status :: 4 - Beta
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3.8
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Classifier: Programming Language :: Python :: 3.9
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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Requires-Python: >=3.8
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Description-Content-Type: text/markdown
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License-File: LICENSE.txt
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Requires-Dist: numpy
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Requires-Dist: pandas
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Requires-Dist: pysam
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A simple tool for measuring chromosome-specific telomeres from long-read alignments.
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[Telometer Github](https://github.com/santiago-es/Telometer)
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LICENSE.txt
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README.md
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pyproject.toml
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telometer/__init__.py
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telometer/telometer.py
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telometer/telometer_variant_support.py
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telometer/variant_support_v2.py
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Metadata-Version: 2.4
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Name: telometer
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Version: 2.0.1
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Summary: Quantitative digital telomere measurement from nanopore long-reads
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Author-email: "Santiago E. Sanchez" <santy.esanchez@gmail.com>
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License-Expression: MIT
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Description-Content-Type: text/markdown
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A simple tool for measuring chromosome-specific telomeres from long-read alignments.
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[Telometer Github](https://github.com/santiago-es/Telometer)
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[project]
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name = "telometer"
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version = "2.0.1"
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description = "Quantitative digital telomere measurement from nanopore long-reads"
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readme = "README.md"
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authors = [
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{ name = "Santiago E. Sanchez", email = "santy.esanchez@gmail.com" }
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]
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classifiers = [
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"Programming Language :: Python :: 3",
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"Operating System :: OS Independent"
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]
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dependencies = [
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"requests",
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"numpy"
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]
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[tool.setuptools.packages.find]
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where = ["."]
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include = ["telometer*"]
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exclude = ["build*", "dist*"]
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@@ -1,16 +0,0 @@
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Metadata-Version: 2.4
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Name: telometer
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Version: 2.0.1
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Summary: Quantitative digital telomere measurement from nanopore long-reads
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Author-email: "Santiago E. Sanchez" <santy.esanchez@gmail.com>
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License-Expression: MIT
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Classifier: Programming Language :: Python :: 3
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.7
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Description-Content-Type: text/markdown
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Requires-Dist: requests
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Requires-Dist: numpy
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A simple tool for measuring chromosome-specific telomeres from long-read alignments.
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[Telometer Github](https://github.com/santiago-es/Telometer)
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