Reading and Writing Files

Open a file with open inside a with block. The block closes the file when it ends, including when an error is raised.

with open("counts.tsv") as handle:
    first_line = handle.readline()
print(first_line.strip())

The sandbox has several files mounted already. counts.tsv and variants.tsv are used in the examples below.

Reading line by line

Looping over the handle reads one line at a time, which works on files too large to fit in memory.

with open("variants.tsv") as handle:
    for line in handle:
        print(line.strip())

Each line keeps its trailing newline, so strip() is almost always needed.

Reading it all at once

with open("counts.tsv") as handle:
    text = handle.read()
print(len(text), "characters")

with open("counts.tsv") as handle:
    lines = handle.read().splitlines()
print(len(lines), "lines")

Splitting columns

A tab-separated line splits on \t.

with open("counts.tsv") as handle:
    header = handle.readline().strip().split("\t")
    print(header)
    for line in handle:
        fields = line.strip().split("\t")
        print(fields[0], fields[1])

Writing

"w" creates or overwrites. "a" appends.

with open("output.txt", "w") as handle:
    handle.write("gene\tdepth\n")
    handle.write("TP53\t120\n")

with open("output.txt") as handle:
    print(handle.read())

Task

Write column_sum(path, column). Read a tab-separated file with a header row, and return the sum of the named column as an integer. Assume the column exists and every value in it is a whole number.