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

@@ -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  

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

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`

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"