Metadata-Version: 1.1
Name: genome_update
Version: 0.1.6
Summary: A script for updating a local directory with genomes, from NCBI assembly files
Home-page: https://github.com/Emisam/genome_update.git
Author: Emil Samuelsson
Author-email: Emil@Samuelsson.pp.se
License: MIT
Description: # genome_update
        
        genome_update is a package that downloads genomes from NCBI and saves information about them in a yaml file.
        It can also use a local yaml file to update and download new genomes.
        
        ## Getting Started
        
        These instructions will provide information how to install and use the software.
        
        ### Prerequisites
        
        Python 3.5
        Pandas
        PyYaml
        
        
        ### Installing
        
        To install Genome_update you can either download source code directly from github and build it your self, an easier alternative is to use pip.
        
        Installing by pip:
        
        ```
        pip install genome_update
        ```
        Pip will also install all prerequisities. It is also recommended to update the prerequisities.
        
        Installing genome_update and upgrading prerequisities: 
        
        ```
        pip install genome_update --upgrade
        ```
        
        ### Usage
        
        Simply download all genomes from a specified genus:
        ```
        genome_update -g <Genus>
        ```
        
        Download all genomes from a specific genus, but much faster:
        ```
        genome_update -g <Genus> -p <threads>
        ```
        
        Download all genomes from a specific genus, but much faster, to a specific directory:
        ```
        genome_update -g <Genus> -p <threads> -o <directory>
        ```
        
        Download all genomes from a specific species:
        ```
        genome_update -g <Genus> -s <species_taxid>
        ```
        
        To update a local yaml file:
        ```
        genome_update -u -i <yamlfile>
        ```
        
        To download missing genomes from a local yaml file:
        ```
        genome_update -d -i <yamlfile>
        ```
        
        To download genomes from another domain than bacteria:
        ```
        genome_update -domain <domain> -g <Genus> 
        ```
        
        
        
        ## Authors
        
        * **Emil Samuelsson** - *Initial work* - [Emisam](https://github.com/Emisam)
        
        
        ## License
        
        This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
        
        ## Acknowledgments
        
        * Would like to thank kblin for his amazing work with the ncbi_genome_download which provided lots of insipration when writing genome_update.
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
