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https://github.com/mikeph52/biogenie

BioGenie is a complete bioinformatics command line tool, written in C++.
https://github.com/mikeph52/biogenie

bioinformatics bioinformatics-pipeline bioinformatics-scripts bioinformatics-software bioinformatics-tool dna dna-sequences pipeline protein rna-seq

Last synced: 3 months ago
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BioGenie is a complete bioinformatics command line tool, written in C++.

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README 

          
# BioGenie

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



Image



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

- To run the app, simply type:

```

biogenie  

```

- For example, to calculate GC percentage:

```

biogenie -gc example.fasta

```



## Documentation

BioGenie uses functions to execute different tools for different applications.

Read [Documentation](documentation.md) for more information (*References included*).

- Get the complement DNA sequence ---> "-c".

- Get the reverse complement DNA sequence ---> "-rc".

- Get the codon number ---> "-nc".

- Get the mRNA ---> "-t".

- Motif search ---> "-mf".

- Ambiguous bases statistics ---> "-amb".

- GC percentage calculation ---> "-gc".

- Generate the aminoacids(Protein chain) ---> "-p".

- Generate the Protein chain with color ---> "-pc".

- Separate different sequencies in a FASTA file ---> "-ss".

- Print the different sequence headers from a FASTA file ---> "-sh".

- Trim DNA sequence ---> "-tr".

- Calculate the Number of Base Pairs(bp) ---> "-bp".

- Get the purine/pyrimidine ratio --> "-pp".

- Calculate melting temperature (Tm) of DNA sequences using the Wallace Rule(only valid for oligos <20bp) ---> "-mt1".

- Calculate melting temperature (Tm) of DNA sequences using the SantaLucia 1998 nearest-neighbor method ---> "-mt2".

- Calculate the Isoelectric Point of a protein ---> "-pi".

- Calculate the molecular weight of a protein(kDa) ---> "-mw".

- Calculate the Extinction Coefficient of a protein ---> "-ec".

- Coloured cDNA sequence ---> "-cc".

- Coloured DNA sequence ---> "-sc".

- Get the Open Reading Frame(ORF) ---> "-orf".

- Generate cDNA sequence FASTA ---> "-cw".

- Generate Reverse cDNA sequence FASTA ---> "-rcw".

- Generate mRNA sequence FASTA ---> "-tw".

- Calculate Codon Usage Bias(CUB) ---> "-cub".

- Export Codon Usage Bias(CUB) to CSV file ---> "-wcub".

- Calculate Hydrogen Bonds of dsDNA ---> "-hb".

- Custom preset pipeline 1 ---> "-pip1".

- Custom preset pipeline 2 ---> "-pip2".

- Custom preset pipeline 3 ---> "-pip3".



More functions will be added in the future.



> [!NOTE]

> _If you have any suggestions for new features or a bug encountered, create an Issue or send me a message at: mikeph526@outlook.com. I'm happy to help._



## Installation

### GNU Linux

- Download BioGenie from Releases, or with wget:

```

wget https://github.com/mikeph52/BioGenie/releases/download/v.0.27.0/biogenie_linux_0.27.0

``` 

- 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

```

- If you need to build from source:

```

git clone https://github.com/mikeph52/BioGenie.git

g++ main.cpp -o biogenie

sudo mv biogenie /usr/local/bin/

```

### macOS

- Download BioGenie from Releases, or with curl:

```

curl -l https://github.com/mikeph52/BioGenie/releases/download/v.0.27.0/biogenie_macos_0.27.0

``` 

- 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

```

- If you need to build from source(probably not):

```

git clone https://github.com/mikeph52/BioGenie.git

g++ -std=c++17 main.cpp -o biogenie

sudo mv biogenie /usr/local/bin/

```

### MS Windows (Deprecated)

> [!IMPORTANT]

> _The Windows version is not being maintained and probably never will. Last available version: 0.14.0(https://github.com/mikeph52/BioGenie/releases/tag/v.0.14.0). Use WSL(Windows Subsystem for Linux) instead._

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. I don't think it is possible to make and maintain a gui version for windows. The code is complicated already. It's time to move on.



## Changelog:

- 0.27.0:

Multi core support added for pip1, pip2 and pip3(https://github.com/mikeph52/BioGenie/issues/30), (https://github.com/mikeph52/BioGenie/issues/31). Ambiguous bases statistics added. Execution timer added. Minor bugs fixed.



- 0.26.0:

Hydrogen bonds calculator and protein chain with color added.

- 0.25.0:

Protein mollecular weight, isoelectric point, extinction coeficient and pipeline 3 added. Issues https://github.com/mikeph52/BioGenie/issues/25, https://github.com/mikeph52/BioGenie/issues/27 fixed. Major performance improvements made. Minor bugs fixed. 

- 0.24.0:

Motif search added. Issues https://github.com/mikeph52/BioGenie/issues/19, https://github.com/mikeph52/BioGenie/issues/21, https://github.com/mikeph52/BioGenie/issues/23, https://github.com/mikeph52/BioGenie/issues/24 fixed. Minor formatting issues fixed.

- 0.23.0:

DNA sequence with color added.

- 0.22.0:

Base Pair calculation added to Pipeline 2. Minor bugs fixed.

- 0.21.0:

Base Pair calculation added. Minor bugs fixed.

- 0.20.0:

Codon Usage Bias(CUB) calculation and export to csv function added.

- 0.19.0:

(https://github.com/mikeph52/BioGenie/issues/15)

Minor bugs fixed.

- 0.18.0:

Generate mRNA FASTA added. Minor format bugs fixed.

- 0.17.3:

(https://github.com/mikeph52/BioGenie/issues/13)

Issue Fixed.

- 0.17.2:

(https://github.com/mikeph52/BioGenie/issues/12)

Issue Fixed.

- 0.17.0:

Generate cDNA FASTA and reverse compliment FASTA function added.

- 0.16.0:

Open Reading Frames finder function added. Minor bugs fixed.

- 0.15.0:

(https://github.com/mikeph52/BioGenie/issues/9)

Fixed Melting Temperature Calculator functiion. SantaLucia 1998 nearest-neighbor method added as "-mt2". Pipeline 2 function also fixed. Now uses SantaLucia 1998 nearest-neighbor method for more accurate calculations. Minor bugs fixed.

- 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:

(https://github.com/mikeph52/BioGenie/issues/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:

(https://github.com/mikeph52/BioGenie/issues/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:

(https://github.com/mikeph52/BioGenie/issues/4)

Documentation fixed.

- 0.6.0:

(https://github.com/mikeph52/BioGenie/issues/3)

Documentation added

- 0.5.0:

(https://github.com/mikeph52/BioGenie/issues/2)

Function operator added.

- 0.4.0:

(https://github.com/mikeph52/BioGenie/issues/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.