Question

I am getting a list of lists from this code, and I just want a list. What am I missing? gene list.csv is a simple csv file with one element per line. This code produces a list of each gene in a separate list like: [['IFNAR2'], ['AKT1'], ['AKT2'], ['IFNAR1']]

gene_list = list(csv.reader(open("genelist.csv")))

Answer 1

If all your file contains are one element per line, don’t use the csv module. Just read the file directly:

gen_list = open('genelist.csv').read().splitlines()

The csv module is used to parse multiple comma, space or tab-separated values per line, and thus each line is returned as a list of columns.

If you must use csv for the file, ‘unwrapping’ the resulting nested lists is easy enough:

gene_list = [g[0] for g in csv.reader(open("genelist.csv"))]

That is a list comprehension, that takes the first column of each row produced by the csv.reader() call.