Metadata-Version: 2.1
Name: screen-assembly
Version: 1.2.3
Summary: screens for presence of genes of interest (GOI) in bacterial assemblies
Home-page: https://github.com/shimbalama/screen_assembly.git
Author: Liam McIntyre
Author-email: shimbalama@gmail.com
License: MIT
Keywords: screen assemblies bacteria gene
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: pandas
Requires-Dist: biopython
Requires-Dist: matplotlib
Requires-Dist: tkinter

# Screen assemblies

Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. Generates multiple CSVs and plots that describe which genes are present and how variable their sequence is. Can use DNA or protein query sequences (GOIs) and DNA contigs/fastas or protein fastas as database (db) to search in. 

## Getting Started

You need one fasta file with all GOIs as the query and a folder with db contigs/fastas. Db files can only have one '.' in the name (i.e., sample_1.fa NOT sample.1.fa) 

### Prerequisites

#### Required

Python 3
Command line blast
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

#### Optional

Clustal Omega
http://www.clustal.org/omega/
IQtree
http://www.iqtree.org/doc/Quickstart

### Installing

pip3 install --user screen_assembly
Make sure screen_assembly3.py is in you PATH

### Check for updates

pip3 install --user screen_assembly

## Running the tests

Once screen_assembly3.py is in your PATH type screen_assembly3.py -h . If you have all dependencies then the help menu will display. Otherwise read the erorr and install whichever dependency is missing.

## Running the program

Please see the WIKI

## Authors

* **Liam McIntyre** - https://github.com/shimbalama/

## License

This project is licensed under the MIT License - see the LICENSE https://github.com/shimbalama/screen_assembly/blob/master/LICENSE file for details

## Acknowledgments

* Mark Davies lab and Jake for testing



