Question

I have lines of data which I want to parse.
The data looks like this:

a score=216 expect=1.05e-06
a score=180 expect=0.0394

What I want to do is to have a subroutine
that parse them and return 2 values (score and expect) for
each line.

However this function of mine doesn’t seem to work:

def scoreEvalFromMaf(mafLines):
    for word in mafLines[0]:
        if word.startswith("score="):
            theScore = word.split('=')[1]
            theEval  = word.split('=')[2]
            return [theScore, theEval]
    raise Exception("encountered an alignment without a score")

Please advice what’s the right way to do it?

Answer 1

It looks like you want to split each line up by spaces, and parse each chunk separately. If mafLines is a string (ie. one line from .readlines():

def scoreEvalFromMafLine(mafLine):
    theScore, theEval = None, None
    for word in mafLine.split():
        if word.startswith("score="):
            theScore = word.split('=')[1]
        if word.startswith("expect="):
            theEval  = word.split('=')[1]

    if theScore is None or theEval is None:
        raise Exception("Invalid line: '%s'" % line)

    return (theScore, theEval)

The way you were doing it would iterate over each character in the first line (since it’s a list of strings) rather than on each space.