BioGenie

BioGenie is a complete bioinformatics command line tool for macOS, GNU Linux and MS Windows, written in C++.

Important

Windows CLI version in Beta. It's not as quick as the other versions. GUI version is available in alpha, but it's still not usable. Available in Releases(https://github.com/mikeph52/BioGenie/releases/tag/testing)

It currently supports fasta formats(.fasta, .fa).

• To run the app, simply type:

biogenie <function> <filename>

• For example, to calculate GC percentage:

biogenie -gc example.fasta

Documentation

BioGenie uses functions to execute different tools for different applications.

• Get the complement DNA sequence ---> "-c".
• Get the reverse complement DNA sequence ---> "-rc".
• Get the codon number ---> "-nc".
• Get the mRNA ---> "-t".
• GC percentage calculation ---> "-gc".
• Generate the aminoacids(Protein chain) ---> "-p".
• Separate different sequencies in a FASTA file ---> "-ss".
• Print the different sequence headers from a FASTA file ---> "-sh".
• Trim DNA sequence ---> "-tr".
• Get the purine/pyrimidine ratio --> "-pp".
• Calculate melting temperature (Tm) of DNA sequences ---> "-mt".
• Custom preset pipeline 1 ---> "-pip1".
• Custom preset pipeline 2 ---> "-pip2".
• Coloured cDNA sequence ---> "-cc".

More functions will be added in the future.

Installation

GNU Linux

• Download BioGenie from Releases, or with wget:

wget https://github.com/mikeph52/BioGenie/releases/download/v.0.14.0/biogenie_linux_0.14.0

• Run "chmod +x" first(Replace 0.x.x with the correct version).

sudo chmod +x biogenie_linux_0.x.x

• Move it to bin folder by executing the following command:

sudo mv biogenie_linux_0.x.x /usr/local/bin/biogenie

macOS

• Download BioGenie from Releases, or with curl:

curl -l https://github.com/mikeph52/BioGenie/releases/download/v.0.14.0/biogenie_macos_0.14.0

• Run "chmod +x" first(Replace 0.x.x with the correct version).

sudo chmod +x biogenie_macos_0.x.x

• Move it to bin folder by executing the following command:

sudo mv biogenie_macos_0.x.x /usr/local/bin/biogenie

MS Windows

It requires Windows 10 or later.

• Download BioGenie from Releases.
• Add the executable to PATH(https://stackoverflow.com/questions/44272416/add-a-folder-to-the-path-environment-variable-in-windows-10-with-screenshots)
• Run from powershell. There's also a GUI Version Available on Alpha testing.

Caution

This is an Alpha testing version. It is not functional. Not for scientific use.

Important

Windows version in Beta. Has a lot of room for improvements. In MS Windows Home Edition, there's a reported bug, causing an exception handle(#8).

Changelog:

• 0.14.0: Coloured cDNA sequence. Minor adjustments made and bugs fixed.
• 0.13.0: Purine/pyrimidine ratio and Melting temperature(Tm) calculator functions added. Preset Pipeline 2 added. Minor format fixes.
• 0.12.2: Minor format fixes.
• 0.12.0: (#7) Protein function output fixed, "Pipeline 1" added and minor bugs fixed.
• 0.11.0: FASTA file verification and integrity checker added.
• 0.10.0: (#6) FASTA sequence header print function added. DNA trimmer function added. Windows support added. Minor bugs fixed and quality of life improvements.
• 0.9.0: Linux support added. FASTA sequencies separator added and minor bugs fixed.
• 0.8.0: Protein chain option added and minor bugs fixed.
• 0.7.0: (#4) Documentation fixed.
• 0.6.0: (#3) Documentation added
• 0.5.0: (#2) Function operator added.
• 0.4.0: (#1) Reverse complement DNA function added.
• 0.3.0: Number of codone calculator added.
• 0.2.3: GC calculator, complimentary DNA and transcripted RNA functions added.
• 0.1.0: First Version.