pyproject.toml

[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "pbiotools"
description = "Miscellaneous bioinformatics and other supporting utilities for Python 3"
readme = "README.md"
license = { text = "MIT" }
authors = [{ name = "Brandon Malone" }]
maintainers = [
  { name = "Etienne Boileau", email = "boileau@uni-heidelberg.de" }
]
keywords = ["bioinformatics", "riboseq"]
# See https://pypi.python.org/pypi?%3Aaction=list_classifiers
classifiers = [
  "Development Status :: 4 - Beta",
  "Intended Audience :: Science/Research",
  "Topic :: Scientific/Engineering :: Bio-Informatics",
  "License :: OSI Approved :: MIT License",
  "Operating System :: MacOS :: MacOS X",
  "Operating System :: POSIX :: Linux",
  "Programming Language :: Python :: 3 :: Only",
  "Programming Language :: Python :: 3.7",
  "Programming Language :: Python :: 3.8",
  "Programming Language :: Python :: 3.9",
  "Programming Language :: Python :: 3.10",
]
dynamic = ["version"]
requires-python = ">=3.7,<3.11"
dependencies = [
  "biopython",
  "dask",
  "fastparquet",
  "joblib",
  "matplotlib",
  "matplotlib_venn",
  "mygene",
  "numpy",
  "openpyxl",
  "pandas",
  "pip",
  "pyensembl",
  "pysam",
  "pytest",
  "seaborn",
  "scikit-learn",
  "scipy",
  "tqdm",
]

[project.scripts]
add-mygene-info-to-orfs = "pbiotools.utils.pgrms.add_mygene_info_to_orfs:main"
bam-to-wiggle = "pbiotools.utils.pgrms.bam_to_wiggle:main"
bedx-to-bedy = "pbiotools.utils.pgrms.bedx_to_bedy:main"
bed12-to-gtf = "pbiotools.utils.pgrms.bed12_to_gtf:main"
convert-ccds-to-bed = "pbiotools.utils.pgrms.convert_ccds_to_bed:main"
count-aligned-reads = "pbiotools.utils.pgrms.count_aligned_reads:main"
count-reads = "pbiotools.utils.pgrms.count_reads:main"
create-mygene-report = "pbiotools.utils.pgrms.create_mygene_report:main"
dna-to-aa = "pbiotools.utils.pgrms.dna_to_aa:main"
download-srr-files = "pbiotools.utils.pgrms.download_srr_files:main"
extract-bed-sequences = "pbiotools.utils.pgrms.extract_bed_sequences:main"
extract-cds-coordinates = "pbiotools.utils.pgrms.extract_cds_coordinates:main"
fasta-to-fastq = "pbiotools.utils.pgrms.fasta_to_fastq:main"
fastq-pe-dedupe = "pbiotools.utils.pgrms.fastq_pe_dedupe:main"
filter-bam-by-ids = "pbiotools.utils.pgrms.filter_bam_by_ids:main"
fix-all-bed-files = "pbiotools.utils.pgrms.fix_all_bed_files:main"
get-all-utrs = "pbiotools.utils.pgrms.get_all_utrs:main"
get-read-length-distribution = "pbiotools.utils.pgrms.get_read_length_distribution:main"
gtf-to-bed12 = "pbiotools.utils.pgrms.gtf_to_bed12:main"
join-long-chromosomes = "pbiotools.utils.pgrms.join_long_chromosomes:main"
merge-isoforms = "pbiotools.utils.pgrms.merge_isoforms:main"
remove-duplicate-bed-entries = "pbiotools.utils.pgrms.remove_duplicate_bed_entries:main"
remove-duplicate-sequences = "pbiotools.utils.pgrms.remove_duplicate_sequences:main"
remove-multimapping-reads = "pbiotools.utils.pgrms.remove_multimapping_reads:main"
reorder-fasta = "pbiotools.utils.pgrms.reorder_fasta:main"
run-bowtie = "pbiotools.utils.pgrms.run_bowtie:main"
run-signalp = "pbiotools.utils.pgrms.run_signalp:main"
run-tmhmm = "pbiotools.utils.pgrms.run_tmhmm:main"
split-bed12-blocks = "pbiotools.utils.pgrms.split_bed12_blocks:main"
split-long-chromosomes = "pbiotools.utils.pgrms.split_long_chromosomes:main"
subtract-bed = "pbiotools.utils.pgrms.subtract_bed:main"

[project.urls]
Github = "https://github.com/dieterich-lab/pbiotools"
Issues = "https://github.com/dieterich-lab/pbiotools/issues"

[project.optional-dependencies]
tests = ["pytest", "pytest-cov"]
docs = [
  "ipykernel",
  "matplotlib",
  "nbsphinx",
  "pandoc",
  "sphinx>=4.5.0",
  "sphinx_rtd_theme>=1.0.0"
]

[tool.setuptools.dynamic]
version = { attr = "pbiotools.__version__" }

[tool.pytest.ini_options]
testpaths = ["tests"]