biopytk 0.2.2

Personal Toolkit for Bioinformatics and Computational Biology pipelines. (WIP)

BioPyTK

Personal Toolkit for Bioinformatics and Computational Biology pipelines. Latest release: v0.1.2

In this README:

• Features
• Usage
  • Initial setup
  • Examples
• FAQ

Features

This package contains the following modules:

⚙️ bio_seq

• DNA/RNA sequencing tools.

__init__()	printSeq()	nucFrequencyDict()
validateSeq()	percentGC()	transcribe()
dnaCompliment()	rnaCompliment()	dna_reverseCompliment()
rna_reverseCompliment()	getBasePairs()	hammingDist()
seqCompare()	translate()	seqSummary()
get_reading_frames()	getAllORFProteins()	globalAlign()

⚙️ aa_seq

• Amino Acid & Polypeptide analysis tools.

  getProteinsFromRF()

⚙️ fasta_tk

• FASTA file analysis tools.
  • Supports: .fasta, .fa file types.
  • More support to come in later releases

percentGC_fasta()	gcContentFromFASTA()	getMaxGCFromFASTA()
dictFromFASTA()	parseFASTA()	dfFromFASTA()

Usage

Initial setup

1. cd to your desired install directory and use pip to install the package.

   pip install biopytk
   

   OR

2. Navigate to the PyPi BioPyTK download page and install manually. Need help installing packages? Click here.

Examples

Coming soon!

FAQ

Can I use this package for my own work?

Absolutely! Please see the License information below.

Will this package work with older versions of Python?

It is recommended to use >Python 3.11.1 as this was the version the package was built on. If future Python releases cause dependency issues, patches will be released.

Why are you making this if BioPython exists?

This is a personal project to practice bioinformatics tooling creation, package management, and overall explore bioinformatics. This is in no way intended to take over large open-source projects, but rather act as a sandbox for personal research and development!

License

Steve-Cheney/biopytk is licensed under the MIT License.

Copyright (c) 2023 Stephen Cheney