Metadata-Version: 2.1
Name: sniffles2_plot
Version: 0.1.1
Summary: a visualizer tool for plot generating
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: seaborn<1,>=0.11.0
Requires-Dist: upsetplot<1,>=0.8.0
Requires-Dist: pandas<2,>=1.1.3
Requires-Dist: matplotlib<4,>=3.3.2

# Sniffles Plot

## Introduction

The Sniffle Plot is a Python program that generates plots for single and multi-sample VCF files.

Type of plots for single sample VCF file:

1. Variant Frequency Spectrum
2. Genotype Frequency
3. SV Size & Type Distribution
4. Comparison of Length of Variants

Type of plots for multi samples VCF file:
    
1. Variant Frequency Spectrum
2. Upset plot for sample intersection
3. SV sites per genome
4. Variant call all SVs
5. Size distribution
6. Heat map for deletion and insertion intersections



## Quick Start
To install this package you can simply run the following command:
```
$ pip3 install sniffles2-plot
```

For running the program for multiple vcf files located in a sepcific directory:
```
$ python3 -m sniffles2_plots -i <VCF_files_folder>
``` 
     
For running the program for a single vcf file:
```
$ python3 -m sniffles2_plots -i <file_name> -o <output_folder>
```
Sample results of output:

<img src="./pictures/del_ins_type_size.jpg" width="200" height="200">
<img src="./pictures/hetamap.jpg" width="200" height="200">

<img src="./pictures/length_variant.jpg" width="200" height="200">
<img src="./pictures/sample_upset.png" width="200" height="200">


