Metadata-Version: 2.1
Name: Chimera_Buster
Version: 1.1.3
Summary: eliminates chimeric reads by comparing the UMI sequences and finding any matches in the 5 prime or 3 prime UMIs and keeping the sequence that has the highest prevalence
Home-page: https://github.com/JessicaA2019/Chimera_Buster
Author: Jessica Lauren ALbert
Author-email: Jessica Lauren Albert <jessica.albert2001@gmail.com>
License: MIT License
        
        Copyright (c) 2024 Jessica Lauren Albert
        
        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.
        
Project-URL: Homepage, https://github.com/JessicaA2019/Chimera_Buster
Keywords: HIV,UMIs,PCR,chimeras,ONT sequencing
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3
Description-Content-Type: text/markdown
License-File: LICENSE.txt

# Chimera_Buster
### Overview
This package takes concensus fasta files from the MrHamer pipeline and eliminates chimeric reads by comparing the UMI sequences and finding any matches in the 5' or 3' UMIs and keeping the sequence that has the highest prevalence.
******************
## Installation
##### Requires python<=3.10
### Quick Install
```bash
pip install Chimera_Buster
```
### Manual Install
```bash
git clone https://github.com/JessicaA2019/Chimera_Buster.git 
cd Chimera_Buster
python setup.py install
```
### Dependencies
Some dependencies currently do not install with Chimera_Buster. Please pip install the following dependencies:
* edlib
* pandas
* multiprocessing
* argparse

### Testing
To test if the installation was successful run the following command with the test files provided:
```bash
Chimera_Buster CB_test_files CB_test
 ```
******************
## Usage
    Chimera_Buster [options] {input_folder_name} {output_file_prefix}
### Inputs
To run the pipeline the following input files are required:
| Input | Description |
| ------ | ------ |
|input_folder_name  |    Designates MrHAMER folder to be filtered. This is required.|
|  output_file_prefix  |  Designates output file prefix. This is required.|
The following input files are optional:
| Arguement | Function |
| ------ | ------ |
|-h, --help |  Prints help message to terminal. |
|-m int, --mismatch int|  Designates the maximum number of mismatched/indel bases allowed when comparing UMIs. Default is 1. |
### Outputs
 The main output files created by the pipeline are:
| Output | Description |
|--------|-------------|
| {output_file_prefix}_chimera_list.txt | A list of all chimeric sample IDs. |
| {output_file_prefix}_nonchimera_list.txt | A list of all nonchimeric sample IDs. |
| {output_file_prefix}_chimeras.csv | A csv of the sample ID, UMI sequences, and cluster counts for each chimeric read. |
| {output_file_prefix}_nonchimeras.csv |  A csv of the sample ID, UMI sequences, and cluster counts for each nonchimeric read. |

**************************
## Help
For issues or bugs, please report them on the [issues page][issues]. 

## License

MIT - Copyright (c) 2024 Jessica Lauren Albert

[//]: # (These are reference links used in the body of this note and get stripped out when the markdown processor does its job. There is no need to format nicely because it shouldn't be seen. Thanks SO - http://stackoverflow.com/questions/4823468/store-comments-in-markdown-syntax)

   [issues]: <https://github.com/JessicaA2019/Chimera_Buster/issues>
