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Create venn diagram from intersection between input files.

Project description

Description

The script gets as input folder that contains separate file for each sample with 3 columns: gene name, p-value and log2 of fold change. The script filter according p-value (default: <=0.05) and log2 fold change (default: >=1) and create venn-diagram between the groups.

The file names within the input folder should to be:

sample1.csv, sample2.csv … (until 6 groups) or sample1.xlsx, sample2.xlsx …

The files must to include the header line: Atnum,pv,log2FC

You can see example of input and output files here: venn-diagram-exmple

Run command

create-venn.py –input-dir YOUR-INPUT-FOLDER –output-dir YOUR-OUTPUT-DIR

You can see another optional parameters with the command (–min-log-fc, –max-p-value, –total_gene_numbers): create-venn.py –help

Python version

This project is currently using Python 2.7

Installation

It is recommended to use virtualenv to create a clean python environment.

To install venn-diagram, use pip:

pip install bbcu.venn-diagram

Credit

The plot of the venn made by: https://github.com/benfred/venn.js

Project details


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