Bioinformatics with Python Cookbook - Second Edition

How to do it...

Follow these steps to get started:

1. Let's start by doing some imports:

import osfrom IPython.display import Imageimport rpy2.robjects as robjectsimport pandas as pdfrom rpy2.robjects import pandas2rifrom rpy2.robjects import default_converterfrom rpy2.robjects.conversion import localconverter

We will be using pandas on the Python side. R DataFrames map very well to pandas.

2. We will read the data from our file using R's read.delim function:

read_delim = robjects.r('read.delim')seq_data = read_delim('sequence.index', header=True, stringsAsFactors=False)#In R:# seq.data <- read.delim('sequence.index', header=TRUE, stringsAsFactors=FALSE)

The first thing that we do after importing is access the read.delim R function, which allows ...