Combining the basics

Dr. Granger is interested in studying the relationship between the length of house-elves’ ears and aspects of their DNA. This research is part of a larger project attempting to understand why house-elves possess such powerful magic. She has obtained DNA samples and ear measurements from a small group of house-elves to conduct a preliminary analysis (prior to submitting a grant application to the Ministry of Magic) and she would like you to conduct the analysis for her (she might know everything there is to know about magic, but she sure doesn’t know much about computers). She has placed the file on the web for you to download.

You might be able to do this analysis by hand in Excel, but counting all of those bases would be a lot of work, and besides Dr. Granger seems to always get funded meaning that you’ll be doing this again soon with a much larger dataset. So, you decide to write a script so that it will be easy to do the analysis again.

Write a Python script that:

1. Imports the data into a list of lists
2. Loops over the rows in the dataset
3. For each row in the dataset checks to see if the ear length is large (>10 cm) or small (<=10 cm) and determines the GC-content of the DNA sequence (i.e., the percentage of bases that are either G or C)
4. Stores this information as table in a nested list (where each row is a list within the outer list) where the first column has the ID for the individual, the second column contains the string ‘large’ or the string ‘small’ depending on the size of the individuals ears, and the third column contains the GC content of the DNA sequence.
5. Exports this table to a CSV (comma delimited text) file titled grangers_analysis_yourname.csv.

This code should use functions to break the code up into manageable pieces. To help you get started here are two functions, one for importing the data from the web, and one for exporting it to a csv file.

def get_file_from_web(url):
    """Imports a comma delimited text file from the web into a list of lists"""
    webpage = urllib.urlopen(url)
    datareader = csv.reader(webpage)
    data = []
    for row in datareader:
        data.append(row)
    return data

def export_to_csv(data, filename):
    """Export list of lists to comma delimited text file"""
	outputfile = open(filename, 'wb')
	datawriter = csv.writer(outputfile)
	datawriter.writerows(data)
	outputfile.close()