-
-
Notifications
You must be signed in to change notification settings - Fork 62
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
27f23e1
commit 94bb1ca
Showing
5 changed files
with
275 additions
and
184 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,201 +1,106 @@ | ||
| Welcome to the DNAnalyzer wiki! | ||
| # Welcome to the DNAnalyzer Wiki! | ||
|
|
||
|  | ||
|
|
||
| > DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, regions susceptible to | ||
| > neurodevelopmental disorders, transcription factors, and regulatory elements. Researchers are working to extract | ||
| > valuable information from such software to better understand human health and disease. Currently, we are working on | ||
| > developing a Command-Line-Interface (CLI) and Graphical User Interface (GUI) that will enable physicians to quickly and | ||
| > more easily interact with the software, enabling them to identify genetic mutations that may cause disease. | ||
| > DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, and regulatory elements. | ||
| > Researchers are working to extract valuable information to better understand human health and disease. | ||
| > Currently, we are developing a Command-Line Interface (CLI) and a Graphical User Interface (GUI) to enable physicians | ||
| > to quickly identify genetic mutations. | ||
| # [Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs) | ||
| ## Documents | ||
| [View Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs) | ||
|
|
||
| ## Contributing | ||
|
|
||
| ### Steps to follow 📜 | ||
|
|
||
| #### 1. Fork it 🍴 | ||
|
|
||
| You can get your own fork (copy) of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork` | ||
| button at the top right of this page. | ||
|
|
||
|  | ||
|
|
||
| #### 2. Clone it 👥 | ||
|
|
||
| You must move to your fork of the repository and clone (download) it to your local machine using | ||
|
|
||
| `$ git clone https://github.com/Your_Username/DNAnalyzer.git` | ||
|
|
||
| This creates a local copy of the repository on your machine. | ||
|
|
||
| After cloning the `DNAnalyzer` repository on GitHub, use the change directory command on Linux and Mac to go to that | ||
| folder. | ||
|
|
||
| ```python | ||
| # This will change directory to a folder DNAnalyzer | ||
| $ cd | ||
| DNAnalyzer | ||
| ``` | ||
|
|
||
| Move to this folder for all other commands. | ||
|
|
||
| Let us now add a reference to the original 'DNAnalyzer' repository using: | ||
|
|
||
| `$ git remote add upstream https://github.com/theabhishek07/DNAnalyzer.git` | ||
|
|
||
| This adds a new remote named **_upstream_**. | ||
|
|
||
| Examine the modifications using: | ||
|
|
||
| ```git | ||
| $ git remote -v | ||
| origin https://github.com/Your_Username/DNAnalyzer.git (fetch) | ||
| origin https://github.com/Your_Username/DNAnalyzer.git (push) | ||
| upstream https://github.com/theabhishek07/DNAnalyzer.git (fetch) | ||
| upstream https://github.com/theabhishek07/DNAnalyzer.git (push) | ||
| ``` | ||
|
|
||
| #### 3. Sync with the Remote 🔄 | ||
|
|
||
| Remember to keep your local repository up to date with the remote repository. | ||
|
|
||
| ```python | ||
| # Fetch all remote repositories and delete any deleted remote branches | ||
| $ git | ||
| fetch - -all - -prune | ||
| # Switch to main branch | ||
| $ git | ||
| checkout | ||
| main | ||
| # Reset local main branch to match upstream repository's main branch | ||
| $ git | ||
| reset - -hard | ||
| upstream / main | ||
| # Push changes to your forked DNAnalyzer repo | ||
| $ git | ||
| push | ||
| origin | ||
| main | ||
| ``` | ||
|
|
||
| #### 4. Create a new branch | ||
|
|
||
| Whenever you want to make a contribution, use the following command to establish a new branch and keep your `main` | ||
| branch uncluttered (i.e. synced with remote branch). | ||
|
|
||
| ```python | ||
| # It will create a new branch <branchname> with name and switch to branch <branchname> | ||
| $ git | ||
| checkout - b < branchname > | ||
| ``` | ||
|
|
||
| To switch to desired branch | ||
|
|
||
| ```python | ||
| # To switch from one folder to other | ||
| $ git | ||
| checkout < branchname > | ||
| ``` | ||
|
|
||
| To add the changes to the branch. Use | ||
|
|
||
| ```python | ||
| # To add all files to branch | ||
| $ git | ||
| add. | ||
| ``` | ||
|
|
||
| Type in a message relevant for the code reviewer using | ||
|
|
||
| ```python | ||
| # This message get associated with all files you have changed | ||
| $ git | ||
| commit - m | ||
| "relevant message" | ||
| ``` | ||
|
|
||
| Now, Push your awesome work to your remote repository using | ||
|
|
||
| ```python | ||
| # To push your work to your remote repository | ||
| $ git | ||
| push - u | ||
| origin < branchname > | ||
| ``` | ||
|
|
||
| Finally, in your browser, navigate to your repository and click `Contribute` amd then `Open Pull Request`. There, please | ||
| provide a title and description, with brevity, that describe your much-appreciated effort. | ||
|
|
||
| ## Contribution Guideline | ||
|
|
||
| - Drop a :star: on the GitHub repository (It's optional)<br/> | ||
|
|
||
| - Before Contribute Please | ||
| read `Contributing_Guidelines.md` | ||
| and `CODE_OF_CONDUCT.md` | ||
|
|
||
| - Create an issue of the project or a feature you would like to add in the project and get the task assigned for | ||
| yourself.(Issue can be any bug fixes or any feature you want to add in this project). | ||
|
|
||
| - Fork the repo to your Github.<br/> | ||
|
|
||
| - Clone the Repo by going to your local Git Client in a particular local folder in your local machine by using this | ||
| command with your forked repository link in place of below given link: <br/> | ||
| `git clone https://github.com/VerisimilitudeX/DNAnalyzer` | ||
| - Create a branch using below command. | ||
| `git branch <your branch name>` | ||
| - Checkout to your branch. | ||
| `git checkout <your branch name>` | ||
| - Add your code in your local machine folder. | ||
| `git add . ` | ||
| - Commit your changes. | ||
| `git commit -m"<add your message here>"` | ||
| - Push your changes. | ||
| `git push --set-upstream origin <your branch name>` | ||
|
|
||
| - Make a pull request! (compare your branch with the owner main branch) | ||
| 1. **Fork it 🍴** | ||
| Get your own fork of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork` button at the top right of this page. | ||
|  | ||
|
|
||
| 2. **Clone it 👥** | ||
| Clone your fork to your local machine: | ||
| ```bash | ||
| git clone https://github.com/Your_Username/DNAnalyzer.git | ||
| cd DNAnalyzer | ||
| ``` | ||
| Then, add a reference to the original repository: | ||
| ```bash | ||
| git remote add upstream https://github.com/theabhishek07/DNAnalyzer.git | ||
| git remote -v | ||
| ``` | ||
|
|
||
| 3. **Sync with the Remote 🔄** | ||
| Keep your local repository up-to-date: | ||
| ```bash | ||
| git fetch --all --prune | ||
| git checkout main | ||
| git reset --hard upstream/main | ||
| git push origin main | ||
| ``` | ||
|
|
||
| 4. **Create a new branch** | ||
| Create a new branch for your contribution: | ||
| ```bash | ||
| git checkout -b <branchname> | ||
| ``` | ||
| To switch branches later: | ||
| ```bash | ||
| git checkout <branchname> | ||
| ``` | ||
| Add changes and commit: | ||
| ```bash | ||
| git add . | ||
| git commit -m "your commit message" | ||
| ``` | ||
| Push your branch: | ||
| ```bash | ||
| git push -u origin <branchname> | ||
| ``` | ||
| Finally, in your browser, navigate to your repository, click **Contribute**, and then **Open Pull Request**. Provide a concise title and description describing your contribution. | ||
|
|
||
| ### Contribution Guideline | ||
|
|
||
| - ⭐ Drop a star on the GitHub repository (optional). | ||
| - Before contributing, please read [`Contributing_Guidelines.md`](Contributing_Guidelines.md) and [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md). | ||
| - Create an issue or propose a feature/bug fix. | ||
| - Fork the repo, clone it, create a branch, add your changes, commit, and push. | ||
| - Make a pull request comparing your branch with the main branch of the repository. | ||
|
|
||
| ## Usage | ||
|
|
||
| #### Command-Line Interface (CLI) Usage | ||
|
|
||
| DNAnalyzer uses CLI arguments instead of `stdin`. For example, you can do: | ||
| ### Command-Line Interface (CLI) Usage | ||
|
|
||
| ``` | ||
| DNAnalyzer uses CLI arguments instead of standard input. For example: | ||
| ```bash | ||
| <executable> assets/dna/random/dnalong.fa --amino=ser | ||
| ``` | ||
|
|
||
| or | ||
|
|
||
| ``` | ||
| ```bash | ||
| <executable> assets/dna/random/dnalong.fa --amino=ser --min=0 --max=100 | ||
| ``` | ||
|
|
||
| Help message (--help): | ||
|
|
||
| To view the help message: | ||
| ```bash | ||
| <executable> --help | ||
|
|
||
| # Output: | ||
| Usage: DNAnalyzer [-hrV] --amino=<aminoAcid> [--find=<proteinFile>] [--max=<maxCount>] [--min=<minCount>] DNA | ||
| DNA The FASTA file to be analyzed. | ||
| --amino=<aminoAcid> The amino acid representing the start of a gene. | ||
| --find=<proteinFile> The DNA sequence to be found. | ||
| -h, --help Show this help message and exit. | ||
| --max=<maxCount> Maximum count of the reading frame. | ||
| --min=<minCount> Minimum count of the reading frame. | ||
| -r, --reverse Reverse the DNA sequence before processing. | ||
| -V, --version Print version information and exit. | ||
| ``` | ||
| Usage: DNAnalyzer [-hrV] --amino=<aminoAcid> [--find=<proteinFile>] | ||
| [--max=<maxCount>] [--min=<minCount>] DNA | ||
| A program to analyze DNA sequences. | ||
| DNA The FASTA file to be analyzed. | ||
| --amino=<aminoAcid> The amino acid representing the start of a gene. | ||
| --find=<proteinFile> The DNA sequence to be found within the FASTA file. | ||
| -h, --help Show this help message and exit. | ||
| --max=<maxCount> The maximum count of the reading frame. | ||
| --min=<minCount> The minimum count of the reading frame. | ||
| -r, --reverse Reverse the DNA sequence before processing. | ||
| -V, --version Print version information and exit. | ||
| ``` | ||
|
|
||
| ## Reports | ||
|
|
||
| [Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf) | ||
|
|
||
| [Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf) | ||
|
|
||
| [Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf) | ||
| - [Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf) | ||
| - [Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf) | ||
| - [Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf) | ||
|
|
||
| ## Samples | ||
|
|
||
| [Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md) | ||
| - [Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md) |
Oops, something went wrong.