Initial commit

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+#env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+dask-worker-space/
+*.egg-info/
+.installed.cfg
+*.egg
+*.err
+*.out
+*.db
+*.py*.sh
+*.tsv
+*.csv
+*.gz*
+
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.pdf
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# DotEnv configuration
+.env
+
+# conda
+.conda
+
+# Database
+*.db
+*.rdb
+
+# Pycharm
+.idea
+
+# Jupyter NB Checkpoints
+.ipynb_checkpoints/
+
+# exclude data from source control by default
+/data/
+
+#snakemake
+.snakemake/
+
+
+# exclude test data used for development
+to_be_deleted/test_data/data/ref
+to_be_deleted/test_data/data/reads
+
+#logs
+logs/
+
+# vscode
+.vscode/
+
+# .java/fonts dir get created when creating fastqc conda env
+.java/
+
+/.vscode/settings.json

CONTRIBUTING.md

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+# Contributing to this project
+
+Thanks for your desire to contribute to this project!
+
+## Preparing your fork
+
+1. Hit 'fork' on Github, creating e.g. `yourname/team-repo`.
+2. Clone your project: `git clone https://github.com/yourname/team-repo.git`.
+3. Create a branch: `cd team-repo; git checkout -b new-feature`.
+
+## Making your changes
+
+1. Add your contributions and please adhere to guidelines set by the programming language or team.
+3. Commit your changes: `git commit -m "Added new feature"` and please be descriptive with git commits!
+
+## Creating Pull Requests
+
+1. Push your commit to get it back up to your fork: `git push origin HEAD`.
+2. Visit Github, click the handy "Pull request" button that it will make upon noticing your new branch.
+3. In the description field, write down issue number (if submitting code fixing an existing issue) or describe the issue + your fix (if submitting a wholly new bugfix).
+4. Hit 'submit' and ask for the repository owner to review.

LICENSE

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+MIT License
+
+Copyright (c) 2022 U-BRITE
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# team-repo-template
+:exclamation: _This top heading should be the name of your project i.e. BiocSwirl or SNVariome. Anything between 2 exclamation marks is intended to be deleted. Any content that isn't a heading or an optional heading can be deleted as well. The structure of this readme is open to any creative changes, but the main components of Background/Data/Usage/Team Members should remain. You're free to add images and get creative about how you want your readme to look._ :exclamation:
+
+:exclamation: _The `configs` and `notebooks` directories are also optional. We recommend taking a look at [cookiecutter for datascience](https://github.com/drivendata/cookiecutter-data-science) or [cookiecutter for computational biology](https://github.com/drivendata/cookiecutter-data-science) to get ideas on structuring your projects. Also, use a `.gitignore` that fits the main programming language of your project._ :exclamation:
+
+## Table of Contents
+
+- [Template](#team-repo-template)
+    - [Background](#Background)
+    - [Data](#data)
+    - [Usage](#usage)
+        - [Installation](#installation)
+        - [Requirements](#requirements) _Can be named Dependencies as well_
+        - [Activate conda environment](#activate-conda-environment) _Optional_
+        - [Steps to run ](#steps-to-run) _Optional depending on project_
+            - [Step-1](#step-1)
+            - [Step-2](#step-2)
+    - [Results](#results) _Optional depending on project_
+    - [Team Members](#team-members)
+
+## Background
+
+:exclamation: _Include background on the project, project description, and significance. This will be converted to your team's abstract by the end of the hackathon. This should be updated by Monday, August 1st to include feedback given._ :exclamation:
+
+## Data
+
+:exclamation: _Discuss the data you used and how it can be accessed._ :exclamation:
+
+## Usage
+
+:exclamation: _How will someone not involved in your project be able to run the code or use it._ :exclamation:
+
+### Installation
+
+:exclamation: _If installation is required, please mention how to do so here._ :exclamation:
+
+Installation simply requires fetching the source code. Following are required:
+
+- Git
+
+To fetch source code, change in to directory of your choice and run:
+
+```sh
+git clone -b main \
+    [email protected]:u-brite/team-repo-template.git
+```
+
+### Requirements
+:exclamation: _Note any software used (including Python or R packages), operating system requirements, etc. and its version so that your project is reproducible. It does not have to be in the below format_ :exclamation:
+
+*OS:*
+
+Currently works only in Linux OS. Docker versions may need to be explored later to make it useable in Mac (and
+potentially Windows).
+
+*Tools:*
+
+- Anaconda3
+    - Tested with version: 2020.02
+
+### Activate conda environment
+:exclamation: _Optional: Depends on project._ :exclamation:
+
+Change in to root directory and run the commands below:
+
+```sh
+# create conda environment. Needed only the first time.
+conda env create --file configs/environment.yaml
+
+# if you need to update existing environment
+conda env update --file configs/environment.yaml
+
+# activate conda environment
+conda activate testing
+```
+
+### Steps to run
+:exclamation: _Optional: Depends on project._ :exclamation:
+
+#### Step 1
+
+```sh
+python src/data_prep.py -i path/to/file.tsv -O path/to/output_directory
+```
+
+#### Step 2
+
+```sh
+python src/model.py -i path/to/parsed_file.tsv -O path/to/output_directory
+```
+
+Output from this step includes -
+
+```directory
+output_directory/
+├── parsed_file.tsv               <--- used for model
+├── plot.pdf- Plot to visualize data
+└── columns.csv - columns before and after filtering step
+
+```
+
+**Note**: The is an example note with a [link](https://github.com/u-brite/team-repo-template).
+
+
+## Results
+:exclamation: _If your project yielded or intends to yield some novel analysis, please include them in your readme. It can be named something other than results as well._ :exclamation:
+
+## Team Members
+
+Tarun Mamidi | [email protected] | Team Leader  
+Shaurita Hutchins | [email protected] | Co-leader

configs/environment.yaml

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+name: testing
+
+channels:
+  - conda-forge
+  - anaconda
+
+dependencies:
+  - python=3.8.5
+  - pandas=1.2.1
+  - numpy=1.18.5
+  - pip
+  - pip:
+    - ray==1.6.0

configs/requirements.txt

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+pandas
+numpy
+streamlit

docs/README.md

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+# docs
+
+:exclamation: _This folder should contain any documentation from powerpoint slides for the final presentation/showcase of project to a website to general notes or other documents._ :exclamation:

notebooks/README.md

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+# notebooks
+
+:exclamation: _Any jupyter notebooks can be hosted here._ :exclamation:

results/README.md

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+# results
+
+:exclamation: _This folder is for computational experiments performed on the data. Ensure any analysis or results are appropriately named (no spaces in names; use underscores or dashes) and in this folder. Also, you may include any figures here or in separate folder._ :exclamation: 

src/README.md

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+# src
+
+This folder is for any source code.