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A simple package for calculating pairwise SNP distances

Project description

# pairsnp-python

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## Installation

The python version can be installed using `pip` or by downloading the repository and running `setup.py`.

At the moment it is only available in python2 but I'm planning on converting it to python3.

```
python -m pip install pairsnp
```

or alternatively download the repository and run

```
cd ./pairsnp/python/pairsnp
python ./setup.py 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.
-o OUTPUT, --out OUTPUT
location of output file.
```



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