Python Programming for Biology: Bioinformatics and Beyond

A compendium of tips

After  more  than  enough  moralising  about  coding  style,  we  get  to  some  simple  tips  of

things in Python that might not be so obvious, especially for newcomers to Python. Some

of the points have been covered in earlier chapters, but we reproduce them here to give a

single resource. This really is just a big list, although we have attempted to split things up

into vague subject categories.

Many  of  the  examples  we  give  here  are  simply  aspects  of  Python  that  are  commonly

overlooked. This may be because non-standard options are easily overlooked, because of

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recent additions to the language or because the code looks a bit scary. An example of the

latter would be the following, where zip(*) is used to extract separate lists of the first and

second elements from a list of 2-tuples. So instead of something like:

data = [(2,5),(6,7),(8,7),(8,4),(2,5),(6,4),(3,2)]

xList = [pair[0] for pair in data]

yList = [pair[1] for pair in data]

You might see:

xList, yList = zip(*data)

Without wishing to suggest anything about whether the zip(*) approach is better, it is a

proper part of the language and is something you see in others’ code, so it is good to be

aware of it.

Python  has  many  features  and  it  is  easy  to  overlook  some  of  them,  even  though  they

might be useful. A very simple example of this is the following for calculating logarithms

in any base, which might be done naturally as soon as one learns about the log() function:

from math import log

y = 1e7

x = log(y) / log(10)

As it happens the base for the logarithm is the second argument to the log() function, so

instead we can do:

from math import log

y = 1e7

x = log(y, 10)

This shows the value of carefully reading the Python documentation.