Metadata-Version: 2.1
Name: screen_assembly
Version: 1.2.7
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
Description: # 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. 
        
        If you use this script in scientific publications, then please reference Davies et al., 2019., Nature Genetics., http://dx.doi.org/10.1038/s41588-019-0417-8
        
        ## 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
        
        If tkinter is missing, do 'sudo apt-get install python3-tk' (on Ubuntu)
        
        ### 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
        
        
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
