Metadata-Version: 2.1
Name: pairsnp
Version: 0.0.7
Summary: A simple package for calculating pairwise SNP distances
Home-page: https://github.com/gtonkinhill/pairsnp/
Author: Gerry Tonkin-Hill
Author-email: g.tonkinhill@gmail.com
License: UNKNOWN
Description: # pairsnp-python
        
        [![Travis-CI Build Status](https://travis-ci.com/gtonkinhill/pairsnp-python.svg?branch=master)](https://travis-ci.com/gtonkinhill/pairsnp-python)
        
        ## Installation
        
        This is a Python3 version of pairsnp written with the help of Simon Frost
        
        ```
        git clone https://github.com/gtonkinhill/pairsnp-python
        cd pairsnp-python
        pip3 install .
        ```
        
        ## Quick Start
        
        The python version can be run from the python interpreter as
        
        ```
        from pairsnp import calculate_snp_matrix, calculate_distance_matrix
        
        sparse_matrix, consensus, seq_names = calculate_snp_matrix(fasta.file.name)
        d = calculate_distance_matrix(sparse_matrix, consensus, "dist", False)
        ```
        
        alternatively if installed using pip it can be used at the command line as
        
        
        ```
        pairsnp -f /path/to/msa.fasta -o /path/to/output.csv
        ```
        
        additional options include
        
        ```
        Program to calculate pairwise SNP distance and similarity matrices.
        
        optional arguments:
          -h, --help            show this help message and exit
          -t {sim,dist}, --type {sim,dist}
                                either sim (similarity) or dist (distance) (default).
          -n, --inc_n           flag to indicate differences to gaps should be
                                counted.
          -f FILENAME, --file FILENAME
                                location of a multiple sequence alignment. Currently
                                only DNA alignments are supported.
          -z, --zipped          Alignment is gzipped.
          -c, --csv             Output csv-delimited table (default tsv).
          -o OUTPUT, --out OUTPUT
                                location of output file.
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
