Functions

A function groups a block of code under a name so it can be reused.

def gc_content(sequence):
    gc = sequence.count("G") + sequence.count("C")
    return gc / len(sequence)


print(gc_content("ATGGCC"))

A function without a return returns None.

Arguments

Arguments can be passed by position or by name. Parameters with a default value may be omitted.

def report(gene, depth, minimum=30):
    status = "pass" if depth >= minimum else "fail"
    return f"{gene} {depth} {status}"


print(report("TP53", 120))
print(report("TP53", 25))
print(report("TP53", 25, minimum=20))
print(report(gene="EGFR", depth=45))

Mutable defaults

A default value is created once, when the function is defined, not each time it is called. A mutable default is therefore shared between calls.

def add_bad(gene, collected=[]):
    collected.append(gene)
    return collected


print(add_bad("TP53"))
print(add_bad("BRCA1"))

Use None instead:

def add_good(gene, collected=None):
    if collected is None:
        collected = []
    collected.append(gene)
    return collected


print(add_good("TP53"))
print(add_good("BRCA1"))

Returning several values

A function can return a tuple, which unpacks on assignment.

def bounds(values):
    return min(values), max(values)


low, high = bounds([30, 12, 45])
print(low, high)

Task

Write summarise(depths). It receives a list of integers and returns a tuple of (count, minimum, maximum, mean). Round the mean to 2 decimal places. Return (0, 0, 0, 0.0) for an empty list.