scanitd 0.9.0__tar.gz

scanitd-0.9.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024, Ting-You Wang
+
+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.

scanitd-0.9.0/PKG-INFO

@@ -0,0 +1,103 @@
+Metadata-Version: 2.1
+Name: scanitd
+Version: 0.9.0
+Summary: ScanITD
+Home-page: https://github.com/ylab-hi/ScanITD
+License: MIT
+Author: Ting-You Wang
+Author-email: tywang@northwestern.edu
+Requires-Python: >=3.9,<4.0
+Classifier: Development Status :: 4 - Beta
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: loguru (>=0.7.0,<0.8.0)
+Requires-Dist: numpy (>=2.0.0,<3.0.0)
+Requires-Dist: psutil (>=5.9.5,<6.0.0)
+Requires-Dist: pyfaidx (>=0.7.2,<0.8.0)
+Requires-Dist: pysam (>=0.22.0,<0.23.0)
+Requires-Dist: rich (>=13.7.0,<14.0.0)
+Requires-Dist: ssw-py (>=1.0.1,<2.0.0)
+Requires-Dist: typer (>=0.12.5,<0.13.0)
+Project-URL: Changelog, https://github.com/ylab-hi/ScanITD/releases
+Project-URL: Documentation, https://scanitd.readthedocs.io
+Project-URL: Repository, https://github.com/ylab-hi/ScanITD
+Description-Content-Type: text/markdown
+
+# ScanITD
+
+[![PyPI version](https://img.shields.io/pypi/v/scanitd.svg)](https://pypi.python.org/pypi/scanitd)
+[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.org/project/scanitd/#files)
+[![license](https://img.shields.io/pypi/l/scanitd.svg)](https://github.com/ylab-hi/ScanITD/blob/main/LICENSE)
+
+- **PyPI**
+
+```bash
+pip install scanitd
+```
+
+# Usage
+
+ Usage: scanitd [OPTIONS]
+
+ ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation
+## Required Arguments
+* `--input`, `-i` PATH
+    - Aligned BAM file
+    - Required
+
+* `--ref`, `-r` PATH
+    - Reference genome in FASTA format (with fai index)
+    - Required
+
+* `--output`, `-o` TEXT
+    - Output VCF file
+    - Required
+
+## Optional Arguments
+* `--mapq`, `-m` INTEGER
+    - Minimum MAPQ in BAM for calling ITD
+    - Default: 15
+
+* `--ao`, `-c` INTEGER
+    - Minimum observation count for ITD
+    - Default: 4
+
+* `--depth`, `-d` INTEGER
+    - Minimum depth to call ITD
+    - Default: 10
+
+* `--vaf`, `-f` FLOAT
+    - Minimum variant allele frequency
+    - Default: 0.1
+
+* `--length` INTEGER
+    - Minimum ITD length to report
+    - Default: 10
+
+* `--aln-mismatches`, `-n` INTEGER
+    - Maximum allowed mismatches for pairwise local alignment
+    - Default: 1
+
+* `--ins-mismatches` INTEGER
+    - Maximum allowed mismatches for insertion-inferred duplication
+    - Default: 2
+
+* `--target`, `-t` TEXT
+    - Limit analysis to targets listed in the BED-format file or a samtools region string
+
+* `--log-level`, `-l` [info|warning|error|debug|trace]
+    - Set the logging level
+    - Default: info
+
+* `--version`, `-v`
+    - Show version and exit
+
+# Citation
+
+Wang TY. and Yang R. [ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation](https://doi.org/10.1093/gigascience/giaa089 "ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation").
+

scanitd-0.9.0/README.md

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+# ScanITD
+
+[![PyPI version](https://img.shields.io/pypi/v/scanitd.svg)](https://pypi.python.org/pypi/scanitd)
+[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.org/project/scanitd/#files)
+[![license](https://img.shields.io/pypi/l/scanitd.svg)](https://github.com/ylab-hi/ScanITD/blob/main/LICENSE)
+
+- **PyPI**
+
+```bash
+pip install scanitd
+```
+
+# Usage
+
+ Usage: scanitd [OPTIONS]
+
+ ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation
+## Required Arguments
+* `--input`, `-i` PATH
+    - Aligned BAM file
+    - Required
+
+* `--ref`, `-r` PATH
+    - Reference genome in FASTA format (with fai index)
+    - Required
+
+* `--output`, `-o` TEXT
+    - Output VCF file
+    - Required
+
+## Optional Arguments
+* `--mapq`, `-m` INTEGER
+    - Minimum MAPQ in BAM for calling ITD
+    - Default: 15
+
+* `--ao`, `-c` INTEGER
+    - Minimum observation count for ITD
+    - Default: 4
+
+* `--depth`, `-d` INTEGER
+    - Minimum depth to call ITD
+    - Default: 10
+
+* `--vaf`, `-f` FLOAT
+    - Minimum variant allele frequency
+    - Default: 0.1
+
+* `--length` INTEGER
+    - Minimum ITD length to report
+    - Default: 10
+
+* `--aln-mismatches`, `-n` INTEGER
+    - Maximum allowed mismatches for pairwise local alignment
+    - Default: 1
+
+* `--ins-mismatches` INTEGER
+    - Maximum allowed mismatches for insertion-inferred duplication
+    - Default: 2
+
+* `--target`, `-t` TEXT
+    - Limit analysis to targets listed in the BED-format file or a samtools region string
+
+* `--log-level`, `-l` [info|warning|error|debug|trace]
+    - Set the logging level
+    - Default: info
+
+* `--version`, `-v`
+    - Show version and exit
+
+# Citation
+
+Wang TY. and Yang R. [ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation](https://doi.org/10.1093/gigascience/giaa089 "ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation").

scanitd-0.9.0/pyproject.toml

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+[tool.poetry]
+name = "scanitd"
+version = "0.9.0"
+description = "ScanITD"
+authors = [
+    "Ting-You Wang <tywang@northwestern.edu>",
+]
+license = "MIT"
+readme = "README.md"
+homepage = "https://github.com/ylab-hi/ScanITD"
+repository = "https://github.com/ylab-hi/ScanITD"
+documentation = "https://scanitd.readthedocs.io"
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+[tool.poetry.urls]
+Changelog = "https://github.com/ylab-hi/ScanITD/releases"
+
+[tool.poetry.dependencies]
+python = "^3.9"
+numpy = "^2.0.0"
+pysam = "^0.22.0"
+pyfaidx = "^0.7.2"
+psutil = "^5.9.5"
+ssw-py = "^1.0.1"
+loguru = "^0.7.0"
+typer = "^0.12.5"
+rich = "^13.7.0"
+
+[tool.poetry.extras]
+
+[tool.poetry.build]
+generate-setup-file = true
+
+[tool.poetry.scripts]
+scanitd = "scanitd.cli.cli:app"
+
+[tool.poetry.group.dev.dependencies]
+ruff = "^0.1.6"
+codespell = "^2.2.2"
+ipdb = "^0.13.11"
+isort = "^5.12.0"
+pytest = "^7.4.3"
+coverage = { extras = ["toml"], version = "^7.3" }
+safety = "^2.1.1"
+mypy = "^1.7"
+typeguard = "^4.1.5"
+xdoctest = { extras = ["colors"], version = "^1.1.2" }
+sphinx = "^7.2.6"
+myst-parser= "3.0.0"
+sphinx-autobuild = "^2021.3.14"
+pre-commit = "^3.3.3"
+flake8 = "^6.1.0"
+black = "^23.3"
+bandit = "^1.7.3"
+flake8-bandit = ">=4.1"
+flake8-bugbear = "^23.9.16"
+flake8-docstrings = "^1.6.0"
+flake8-rst-docstrings = "^0.3.0"
+pep8-naming = "^0.13.2"
+reorder-python-imports = "^3.8.2"
+pre-commit-hooks = "^4.3.0"
+sphinx-rtd-theme = "^1.3.0"
+sphinx-click = "^5.0.1"
+Pygments = "^2.17.1"
+pytest-mock = "^3.11.1"
+nox = "^2023.4.22"
+flake8-broken-line = "^1.0.0"
+flake8-comprehensions = "^3.13.0"
+flake8-eradicate = "^1.5.0"
+flake8-simplify = "^0.21.0"
+pynvim = "^0.4.3"
+flake8-2020 = "^1.8.1"
+flake8-alfred = "^1.1.1"
+cohesion = "^1.0.0"
+
+
+[tool.mypy]
+strict = false
+pretty = true
+show_column_numbers = true
+show_error_codes = true
+show_error_context = true
+exclude = "cppext"
+allow_untyped_calls = true
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+norecursedirs = ["cppext"]
+
+[tool.bandit]
+exclude_dirs = ['tests']
+skips = ["B602", "B404", "B603"]
+
+[tool.isort]
+profile = "black"
+
+[tool.ruff]
+lint.select = [
+    # "ANN",
+    # "D",
+    "A",
+    "F",
+    "E",
+    "W",
+    "C90",
+    "I",
+    "UP",
+    "N",
+    "YTT",
+    "TID",
+    "S",
+    "BLE",
+    "FBT",
+    "PLR",
+    "B",
+    "B9",
+    "A",
+    "C4",
+    "T10",
+    "EM",
+    "ICN",
+    "T20",
+    "Q",
+    "RET",
+    "SIM",
+    "ARG",
+    "DTZ",
+    "ERA",
+    "PD",
+    "PGH",
+    "PLC",
+    "PLE",
+    "PLW",
+    "RUF",
+    "PL",
+    "TD",
+    "FIX",
+    "PTH",
+    "TCH",
+    "SLOT",
+    "PT",
+    "PYI",
+    "PIE",
+    "ISC",
+    "FA",
+    "EXE",
+    # "CPY",
+    "COM",
+]
+line-length = 200
+exclude = ["tests"]
+lint.ignore = [
+    "ANN001",
+    "D203",
+    "D213",
+    "PGH003",
+    "PLR0911", # Too many return statements
+    "PLR0913", # Too many arguments to function call
+    "PLR0912", # Too many branches
+    "PLR0915", # Too many statements
+    "DTZ005",  # Without `tz` argument
+    "C901",    # Too complex
+    'PLC0415',
+    'PLR1702',
+    'PLR0917',
+    # formater conflict
+    'COM812',
+    'COM819',
+    'D206',
+    'ISC001',
+    'Q000',
+    'Q001',
+    'Q002',
+    'Q003',
+    'W191',
+    "PLR0904",
+]
+target-version = "py310"
+
+
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+# Like Black, respect magic trailing commas.
+# magic-trailing-comma = "respect"
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+
+[tool.ruff.lint.per-file-ignores]
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+tag_format = "$version"
+version_scheme = "pep440"
+version_provider = "poetry"
+major_version_zero = true
+
+[build-system]
+requires = ["poetry-core>=1.6.0", "setuptools>=68.0.0"]
+build-backend = "poetry.core.masonry.api"

scanitd-0.9.0/setup.py

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+# -*- coding: utf-8 -*-
+from setuptools import setup
+
+package_dir = \
+{'': 'src'}
+
+packages = \
+['scanitd',
+ 'scanitd.base',
+ 'scanitd.cli',
+ 'scanitd.inference',
+ 'scanitd.writer']
+
+package_data = \
+{'': ['*']}
+
+install_requires = \
+['loguru>=0.7.0,<0.8.0',
+ 'numpy>=2.0.0,<3.0.0',
+ 'psutil>=5.9.5,<6.0.0',
+ 'pyfaidx>=0.7.2,<0.8.0',
+ 'pysam>=0.22.0,<0.23.0',
+ 'rich>=13.7.0,<14.0.0',
+ 'ssw-py>=1.0.1,<2.0.0',
+ 'typer>=0.12.5,<0.13.0']
+
+entry_points = \
+{'console_scripts': ['scanitd = scanitd.cli.cli:app']}
+
+setup_kwargs = {
+    'name': 'scanitd',
+    'version': '0.9.0',
+    'description': 'ScanITD',
+    'long_description': '# ScanITD\n\n[![PyPI version](https://img.shields.io/pypi/v/scanitd.svg)](https://pypi.python.org/pypi/scanitd)\n[![PyPI - Wheel](https://img.shields.io/pypi/wheel/scanitd)](https://pypi.org/project/scanitd/#files)\n[![license](https://img.shields.io/pypi/l/scanitd.svg)](https://github.com/ylab-hi/ScanITD/blob/main/LICENSE)\n\n- **PyPI**\n\n```bash\npip install scanitd\n```\n\n# Usage\n\n Usage: scanitd [OPTIONS]\n\n ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation\n## Required Arguments\n* `--input`, `-i` PATH\n    - Aligned BAM file\n    - Required\n\n* `--ref`, `-r` PATH\n    - Reference genome in FASTA format (with fai index)\n    - Required\n\n* `--output`, `-o` TEXT\n    - Output VCF file\n    - Required\n\n## Optional Arguments\n* `--mapq`, `-m` INTEGER\n    - Minimum MAPQ in BAM for calling ITD\n    - Default: 15\n\n* `--ao`, `-c` INTEGER\n    - Minimum observation count for ITD\n    - Default: 4\n\n* `--depth`, `-d` INTEGER\n    - Minimum depth to call ITD\n    - Default: 10\n\n* `--vaf`, `-f` FLOAT\n    - Minimum variant allele frequency\n    - Default: 0.1\n\n* `--length` INTEGER\n    - Minimum ITD length to report\n    - Default: 10\n\n* `--aln-mismatches`, `-n` INTEGER\n    - Maximum allowed mismatches for pairwise local alignment\n    - Default: 1\n\n* `--ins-mismatches` INTEGER\n    - Maximum allowed mismatches for insertion-inferred duplication\n    - Default: 2\n\n* `--target`, `-t` TEXT\n    - Limit analysis to targets listed in the BED-format file or a samtools region string\n\n* `--log-level`, `-l` [info|warning|error|debug|trace]\n    - Set the logging level\n    - Default: info\n\n* `--version`, `-v`\n    - Show version and exit\n\n# Citation\n\nWang TY. and Yang R. [ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation](https://doi.org/10.1093/gigascience/giaa089 "ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation").\n',
+    'author': 'Ting-You Wang',
+    'author_email': 'tywang@northwestern.edu',
+    'maintainer': 'None',
+    'maintainer_email': 'None',
+    'url': 'https://github.com/ylab-hi/ScanITD',
+    'package_dir': package_dir,
+    'packages': packages,
+    'package_data': package_data,
+    'install_requires': install_requires,
+    'entry_points': entry_points,
+    'python_requires': '>=3.9,<4.0',
+}
+
+
+setup(**setup_kwargs)

scanitd-0.9.0/src/scanitd/__init__.py

@@ -0,0 +1,5 @@
+"""Top-level package for ScanITD."""
+
+__author__ = """Ting-You Wang"""
+__version__ = "0.9.0"
+__PACKAGE_NAME__ = "ScanITD"

scanitd-0.9.0/src/scanitd/base/__init__.py

@@ -0,0 +1,27 @@
+"""Init file for scanitd2.
+
+@Filename:    __init__.py
+"""
+
+from .basic import (
+    CigarCode,
+    Event,
+    Interval,
+    Intervals,
+    MappingMode,
+    MicroRegion,
+    Strand,
+)
+from .basic_read import Read, reverse_complement
+
+__all__ = [
+    "CigarCode",
+    "Event",
+    "Interval",
+    "Intervals",
+    "MappingMode",
+    "MicroRegion",
+    "Read",
+    "Strand",
+    "reverse_complement",
+]