The active development version of the degenerate bases algorithm that supports GUI.
This project was developed to analyze oligonucleotide sequences containing degenerate bases and generate a file with all possible outcomes with non-degenerate bases considering the conversion of degenerate bases into conventional bases.
Currently, this project only supports Windows builds, so if you're looking for the version without a graphical user interface, and consequently, "cross-platform", visit the legacy repository.
You can find more information about the algorithm itself here.
These instructions are aimed towards getting you a copy of the project up and running on your local machine for development and testing purposes.
In order to build this project, you'll need to download the following dependencies and IDEs:
Make sure to install the MSVC compiler when installing Qt.
It is fairly easy to install the project, all you need to do is to clone it from GitHub. There is also the option to download a copy of the repository.
If you want to clone the repository using the terminal instead, use:
git clone https://github.com/DatDarkAlpaca/Degenerate-Bases-NoGUI/
Once everything is downloaded, open the solution Degenerate-Bases.sln, click on Extensions and Manage Extensions. A dropdown list will show up. You'll need to install the Qt Visual Studio Tools extension. You may need to restart Visual Studio.
Once installed, open the versions menu under Extensions > Qt VS Tools > Qt Version, then click on the plu sign, and select the qmake.exe path from your Qt installation. It can usually be found under C:\Qt\Version\msvc...\bin\qmake.exe.
To build the project, click Build then Build Solution on Visual Studio. Alternatively, you can use the shortcut Ctrl+Shift+B.
The executable files are generated under bin/Configuration/Platform, and the intermediate files are generated under intermediate/Configuration/Platform.
Once you run the application, a folder called results and a file called settings.ini will be generated in the current directory.
They will be recreated if you delete them.
This program offers you a certain degree of customization regarding the folder which you want to save your results, the pattern used in the fasta results, the size of the chunks that will be written or whether you need extra information about the execution.
The following table lists the settings which you can modify on the settings.ini folder.
You will need to restart the application in order to apply the settings.
| Default | Entry Name | Description |
|---|---|---|
| > | header_character | The initiation character on the outcome's header. |
| seq | header_template | The template name for the outcome's header. |
| Result_ | results-prefix | The template name of the generated files. |
| fas | results-format | The file type which the file will be generated as. |
| ./results/ | results-directory | The directory where the results will be saved on. |
| 1024 | chunk_size | The size of outcome chunks that will be written to the file. |
| false | debug-enable | Displays additional information about the program at the end of the execution. |
| false | chunk_size | A feature designed for testing the chunk writting system. |
The following table lists the available bases.
| Base | Outcomes |
|---|---|
| N | A, C, G, T |
| D | A, G, T |
| V | A, C, G |
| B | C, G, T |
| H | A, C, T |
| W | A, T |
| S | C, G |
| K | G, T |
| M | A, C |
| Y | C, T |
| R | A, G |
| A | A |
| C | C |
| G | G |
| T | T |
| . | . |
| - | - |
| * | * |
This project is licensed under the MIT License - see the LICENSE file for details