Metadata-Version: 2.1
Name: geneutils
Version: 0.0.1
Summary: CLI and utilities for Genetic analysis and database interface
Home-page: https://github.com/samapriya/geneutils
Author: Samapriya Roy
Author-email: samapriya.roy@gmail.com
License: MIT
Description: # geneutils
        
        [![PyPI version](https://badge.fury.io/py/geneutils.svg)](https://badge.fury.io/py/geneutils)
        ![CI geneutils](https://github.com/samapriya/geneutils/workflows/CI%20geneutils/badge.svg)
        
        This tool was originally inspired by the [work here](https://github.com/Gurdhhu/bioinf_scripts) for dealing with nucleotide sequences and more tools will be added as needed. This toolbox requires python 3 and can be installed.
        
        ## Table of contents
        * [Installation](#installation)
        * [geneutils cli tools](#geneutils-cli-tools)
            * [blasthit](#blasthit)
        
        
        ## Installation
        This assumes that you have native python 3 & pip installed in your system, you can test this by going to the terminal (or windows command prompt) and trying
        
        ```python``` and then ```pip list```
        
        If you get no errors and you have python 3 or higher you should be good to go. To install **geneutils** you can install using two methods
        
        ```pip install geneutils```
        
        or you can also try
        
        ```pip install geneutils --user```
        
        or you can also try
        
        ```
        git clone https://github.com/samapriya/geneutils.git
        cd geneutils
        python setup.py install
        ```
        
        Installation is an optional step; the application can be also run directly by executing pydrop.py script. The advantage of having it installed is being able to execute porg as any command line tool. I recommend installation within virtual environment. If you don't want to install, browse into the geneutils folder and try ```python geneutils.py -h``` to get to the same result.
        
        ## geneutils cli tools
        This is a command line tool and it is designed to simply call the tools you need.
        
        ![geneutils_main](https://user-images.githubusercontent.com/6677629/89102487-b2d5b200-d3d7-11ea-937e-cd6e661de31c.gif)
        
        ### blasthit
        This script is intended for taxonomic annotation of **blast** results (blastn, tblastn, blastp or blastx) saved in **Hit Table CSV** format where GenBank accession numbers are in the 4th column. It uses **efetch** function from **Bio.Entrez** package to get information about accessions from **GenBank Nucleotide (Nuccore)** or **Protein** databases.
        The output is an annotated CSV file "*_annotated.csv" with the following columns added:
        
        * Record name
        * Species name
        * Full taxonomy
        * Reference
        * Date of update
        
        ![geneutils_bhits](https://user-images.githubusercontent.com/6677629/89102488-b701cf80-d3d7-11ea-8f1b-b26886563e84.gif)
        
        | arguments | description |
        | --- | --- |
        | path | Pathway to csv-formatted Hit Table file with blastn results. Positional argument |
        | db | For the output of **nucleotide blast** or **tblastn**, use <code>n</code>. For the output of **protein blast** or **blastx**, use <code>p</code>. Positional argument |
        | email | Your NCBI email. Positional argument |
        | -h, --help | Show help message and exit. Optional argument |
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
