pairsnp 0.0.7

Description:

pairsnp 0.0.7

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.