bioinfor_tools

Introduction

bioinfor_tools: A simple tool for setting up bioinformatics pipelines. It is mainly used to quickly call shell commands within python scripts, and provides features such as thread number and qsub.

Install

pip install bioinfor-tools

Quick Guide

import bioinfor_tools as bt
import random

# Decorate a function that generates a Linux command.
@bt.cmd_wrapper(n_jobs=2)
def foo(a='hello'):
    cmd_list = ['sleep {} && echo done!'.format(random.randint(3, 5)) for _ in range(6)]
    return cmd_list, a

foo()

# using qusb.
@bt.cmd_wrapper(n_jobs=2,use_qsub=True)
def foo2(a='hello'):
    cmd_list = ['sleep {} && echo done!'.format(random.randint(3, 5)) for _ in range(6)]
    return cmd_list, a

foo2()