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1 | 1 | # Python tools for Codon Usage Bias Analysis |
2 | | -- This repository hosts different Python3 command-line programs for calculating popular codon usage and amino acid usage frequency statistics from FASTA sequence files (.fasta). |
3 | | -- To use these tools , all that needs to be done is to install python3 and then download the executable binary file <b>(.pyz)</b> from the tool's folder in this repo. |
| 2 | +- This repository hosts different Python3 command-line programs and new graphical user interface web app! for calculating popular codon usage and amino acid usage frequency statistics from FASTA sequence files (.fasta). |
| 3 | +- Quickest way to use these tools is to install python3.10 (or higher via anaconda) and then download the executable binary file <b>(.pyz)</b> from the tool's folder in this repo. |
4 | 4 | - <b> Motivation </b>: I worked with hundreds of genomes so I wrote these scripts to handle batch processing of multiple genomes/ input files and outputs a CSV formatted table that is easier to parse and amenable to statistical analysis like PCA - a task that I found tedious because previously published tools would output the conventional wide-form codon usage table that needed extra processing. |
5 | 5 | - <b> Genomics Publications that used Codon-Usage-inPython <b>: |
6 | 6 | <ul> |
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18 | 18 |
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19 | 19 |
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20 | 20 | # Software Setup: |
21 | | -- All tools require python3 version 3.8 or higher is installed and pandas version 2.0 or higher. |
| 21 | +- All tools require python3 version 3.10 or higher is installed and pandas version 2.0 or higher. |
22 | 22 | - Recommended to install python3 via anaconda https://docs.anaconda.com/anaconda/install/index.html |
23 | 23 |
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24 | 24 | - <font color='green'> See </font> the ```test_data``` folder for examples of the outputs of each tool on the same input fasta file ('NB_CDS.fasta') |
25 | | -# ------How to Use Each Tool ------ |
| 25 | +# ------How to the Codon Usage Web App ------ |
| 26 | +1. Open Terminal (Mac/Linux) or Command Prompt (Windows) |
| 27 | +2. Clone the repository: |
| 28 | + ```bash |
| 29 | + git clone https://github.com/rhondene/Codon-Usage-in-Python.git |
| 30 | + ``` |
| 31 | +3. Navigate to the project folder: |
| 32 | + ```bash |
| 33 | + cd Codon-Usage-in-Python/codon-usage-gui |
| 34 | + ``` |
| 35 | +4. Install the package: |
| 36 | + ```bash |
| 37 | + pip install -e . |
| 38 | + ``` |
| 39 | +### Step 2: Launch the Browser based Web App |
| 40 | +Open your terminal and type: |
| 41 | +```bash |
| 42 | +codon-usage-gui |
| 43 | +``` |
| 44 | +A web page will automatically open in your browser! |
| 45 | +If not, just click on the `Local URL: http://localhost:xxx` to surface the web page |
| 46 | +<img width="639" height="343" alt="image" src="https://github.com/user-attachments/assets/f8fdb52b-d60b-47b7-8e40-26b7ff64be63" /> |
| 47 | + |
| 48 | + |
| 49 | +# ------How to Use Each Command-line Tool ------ |
26 | 50 |
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27 | 51 | ### Compute_RSCU_gene : |
28 | 52 | - Computes relative synonymous codon usage of each 59 degenerate codons per each coding sequence (CDS) according to Sharp and Li, 1986 PMCID: PMC340524 |
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