Metadata-Version: 2.1
Name: IBSpy
Version: 0.1.0
Summary: A package to detect IBS regions
Home-page: https://github.com/Uauy-Lab/IBSpy
Author: Ricardo H. Ramirez-Gonzalez
Author-email: ricardo.ramirez-gonzalez@jic.ac.uk
License: UNKNOWN
Description: # IBSpy
        
        ![Python package](https://github.com/Uauy-Lab/IBSpy/workflows/Python%20package/badge.svg)
        [![Maintainability](https://api.codeclimate.com/v1/badges/5a4b1b0e89f7f9f8c34c/maintainability)](https://codeclimate.com/github/Uauy-Lab/IBSpy/maintainability)
        
        Python library to identify Identical By State regions
        
        ## Installyng IBSpy
        
        There easiest way to install IBSpy is to use pip3. 
        
        ```sh
        pip3 install IBSpy
        ```
        
        
        If ```pip3``` fails, you can clone the project and compiling it with:
        
        ```sh
        pip3 install cython biopython pyfaidx
        python3 setup.py develop
        ```
        
        Then you should have the  IBSpy command available. 
        
        
        ## Preparing the databases
        
        IBSpy requires to have a kmer database from the sequencing files. Currently two formats are supported:
        
          1. Jellyfish: Follow the instructions in its [website](https://github.com/gmarcais/Jellyfish/blob/master/doc/Readme.md)
          2. kmerGWAS: Has an adhoc file format that contains only the kmers in a binary representation, sorted. This option is faster than the jellyfish version, but creating the kmer table is less straight forward. The manual is [here](https://github.com/voichek/kmersGWAS/blob/master/manual.pdf).
        
        ## Running IBSPy
        
        IBSpy has relatively few options, you can look at them with the ```---help``` command. 
        
        ```sh
        IBSPy --help
        usage: IBSPy [-h] [-w WINDOW_SIZE] [-k KMER_SIZE] [-d DATABASE] [-r REFERENCE]
                     [-z] [-o OUTPUT] [-f {kmerGWAS,jellyfish}]
        
        optional arguments:
          -h, --help            show this help message and exit
          -w WINDOW_SIZE, --window_size WINDOW_SIZE
                                window size to analyze
          -k KMER_SIZE, --kmer_size KMER_SIZE
                                Kmer size of the database
          -d DATABASE, --database DATABASE
                                Kmer database
          -r REFERENCE, --reference REFERENCE
                                The reference with the position of the kmers
          -z, --compress        When an ouput file is present, it is compressed as .gz
          -o OUTPUT, --output OUTPUT
                                Output file. If missing, the ouptut is sent to stdout
          -f {kmerGWAS,jellyfish}, --database_format {kmerGWAS,jellyfish}
                                Database format (kmerGWAS, jellyfish)
        ```
        
        To generate the table with the number of observed kmers and variants run the following command, using the kmer database from kmerGWAS use the following command:
        
        ```sh
         IBSpy --output "kmer_windows_LineXXX.tsv.gz" -z --database kmers_with_strand  --reference arinaLrFor.fa --window_size 50000 --compress
        ```
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
