From 42308456fa5481046d3d2066a8cc84fa4fbf0acf Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Mon, 22 Mar 2021 12:12:21 +0100 Subject: [PATCH] v0.1.3 update for GitHub (#68) * Updated CHANGELOG * Fixed link and added find_seq example * Updated shields. * Updated shields. * Changed find_seq description. * Shortened find_seq description * Updated copyright year. * Updated requirements.txt for dependency graph on GitHub. --- CHANGELOG.md | 5 +++++ LICENSE | 2 +- README.md | 13 +++++++------ requirements.txt | 26 ++++++++++++++++++++++++++ 4 files changed, 39 insertions(+), 7 deletions(-) create mode 100644 requirements.txt diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b5faf7..b7d469b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [Unreleased] +## [0.1.3] +### Fixed +- Cleaned dependencies, solved linting and packaging issues. + ## [0.1.2] ### Fixed - Bug in flagstats export. @@ -49,6 +53,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [0.0.1] - 2020-08-03 [Unreleased]: https://github.com/ggirelli/fastx-barber/tree/dev +[0.1.2]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.3 [0.1.2]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.2 [0.1.1]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.1 [0.1.0]: https://github.com/ggirelli/fastx-barber/releases/tag/v0.1.0 diff --git a/LICENSE b/LICENSE index 1c2f746..f1d3763 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2020 Gabriele Girelli +Copyright (c) 2020-21 Gabriele Girelli Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 14cfe01..8a17cb7 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,9 @@ # fastx-barber -[![DOI](https://zenodo.org/badge/281703558.svg)](https://zenodo.org/badge/latestdoi/281703558) ![](https://img.shields.io/librariesio/github/ggirelli/fastx-barber.svg?style=flat) ![](https://img.shields.io/github/license/ggirelli/fastx-barber.svg?style=flat) -![](https://github.com/ggirelli/fastx-barber/workflows/Python%20package/badge.svg?branch=main&event=push) ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/fastx-barber) ![PyPI - Format](https://img.shields.io/pypi/format/fastx-barber) ![PyPI - Status](https://img.shields.io/pypi/status/fastx-barber) -![](https://img.shields.io/github/release/ggirelli/fastx-barber.svg?style=flat) ![](https://img.shields.io/github/release-date/ggirelli/fastx-barber.svg?style=flat) ![](https://img.shields.io/github/languages/code-size/ggirelli/fastx-barber.svg?style=flat) -![](https://img.shields.io/github/watchers/ggirelli/fastx-barber.svg?label=Watch&style=social) ![](https://img.shields.io/github/stars/ggirelli/fastx-barber.svg?style=social) +[![DOI](https://zenodo.org/badge/281703558.svg)](https://zenodo.org/badge/latestdoi/281703558) ![Release ID](https://img.shields.io/github/release/ggirelli/fastx-barber.svg?style=flat) ![Release date](https://img.shields.io/github/release-date/ggirelli/fastx-barber.svg?style=flat) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/fastx-barber) ![PyPI - Status](https://img.shields.io/pypi/status/fastx-barber) ![GitHub Actions Python package status](https://github.com/ggirelli/fastx-barber/workflows/Python%20package/badge.svg?branch=main&event=push) +![license](https://img.shields.io/github/license/ggirelli/fastx-barber.svg?style=flat) ![Code size](https://img.shields.io/github/languages/code-size/ggirelli/fastx-barber.svg?style=flat) +![Watch no.](https://img.shields.io/github/watchers/ggirelli/fastx-barber.svg?label=Watch&style=social) ![Stars no.](https://img.shields.io/github/stars/ggirelli/fastx-barber.svg?style=social) [PyPi](https://pypi.org/project/fastx-barber/) | [docs](https://ggirelli.github.io/fastx-barber/) @@ -15,7 +15,7 @@ A Python3.6.13+ package to trim and extract flags from FASTA and FASTQ files. * Selects reads based on a pattern (regex). * Trims reads by pattern (regex), length, or single-base quality. * Extracts parts (flags) of reads based on a pattern and stores them in the read headers. -* [Generates BED file with the locations of a substring](usage#find-sequence) in FASTX records. +* [Generates BED file with the locations of a substring](https://ggirelli.github.io/fastx-barber/usage#find-sequence) in FASTX records. * Regular expression support [*fuzzy* matching](https://pypi.org/project/regex/#approximate-fuzzy-matching-hg-issue-12-hg-issue-41-hg-issue-109) (*fuzzy matching* might affect the barber's speed). * Parallelizes processing by splitting the fastx file in chunks. @@ -36,6 +36,7 @@ Once you have `pipx` ready on your system, install the latest stable release of Run: * `fbarber` to access the barber's services. +* `fbarber find_seq` to extract the locations of a sequence (e.g., restriction site) in FASTX records. * `fbarber flag` to extract or manipulate read flags. * `fbarber match` to select reads based on a pattern (regular expression). * `fbarber trim` to trim your reads. @@ -48,4 +49,4 @@ We welcome any contributions to `fastx-barber`. In short, we use [`black`](https ## License -`MIT License - Copyright (c) 2020 Gabriele Girelli` +`MIT License - Copyright (c) 2020-21 Gabriele Girelli` diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..efa31f0 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,26 @@ +atomicwrites==1.4.0; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.4.0" +attrs==20.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +biopython==1.78; python_version >= "3.6" +colorama==0.4.4; python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and python_version < "4.0" or sys_platform == "win32" and python_version >= "3.6" and python_full_version >= "3.5.0" and python_version < "4.0" +commonmark==0.9.1; python_version >= "3.6" and python_version < "4.0" +dataclasses==0.8; python_version >= "3.6" and python_version < "3.7" +importlib-metadata==3.7.3; python_version < "3.8" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.4.0" and python_version >= "3.6" and python_version < "3.8") +iniconfig==1.1.1; python_version >= "3.6" +joblib==1.0.1; python_version >= "3.6" +numpy==1.19.5; python_version >= "3.6" +packaging==20.9; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pandas==1.1.5; python_full_version >= "3.6.1" +pluggy==0.13.1; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pygments==2.8.1; python_version >= "3.6" and python_version < "4.0" +pyparsing==2.4.7; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6" +pytest==6.2.2; python_version >= "3.6" +python-dateutil==2.8.1; python_full_version >= "3.6.1" +pytz==2021.1; python_full_version >= "3.6.1" +regex==2021.3.17 +rich==9.13.0; python_version >= "3.6" and python_version < "4.0" +six==1.15.0; python_full_version >= "3.6.1" +toml==0.10.2; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.6" +tqdm==4.59.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") +typing-extensions==3.7.4.3; python_version >= "3.6" and python_version < "3.8" +zipp==3.4.1; python_version < "3.8" and python_version >= "3.6"