Python Programming for Biology: Bioinformatics and Beyond

Module

Description

Example

---

fft

A module with methods to perform Fourier

analysis, such as the discrete Fourier

transform and its inverse.

from numpy import

exp, pi, arange

I = complex(0, 1)

t = arange(0.0, 5.0,

0.1)

decay = 0.3

x = exp(2*pi*I*t) *

exp(-decay*t)

w = fft.fft(x)

z = fft.ifft(w)

# z = x up to

numerical error

linalg

A module with methods to perform array

operations common in linear (matrix)

algebra, for example, to calculate

determinant, eigenvalues, eigenvectors,

inverse, single value decomposition etc.

m1 = array([[-1, 1],

[ 2, 3]])

linalg.eig(m1)

linalg.det(m1)

linalg.inv(m1)

linalg.svd(m1)

random

A module with methods for generating and

sampling (pseudo-)random numbers.

vals = random.rand(6)

# Six floats from 0.0

to 1.0

vals =

random.randint(2,9,5)

# Five ints in range

2 to 5

x = [1,2,3,4]

random.shuffle(x)

# New order

random.seed()

# Init pseudorandom

generator

---

Appendix 4

String formatting

Old-style formatting

The following table describes old-style string formatting codes, which are used in Python

strings  which  are  followed  by  the  ‘%’  format  operator,  such  as  ‘%8.3f’  %  value.  These

follow the general system used by sprintf/printf in the standard C library. The general form

of the formatting code syntax is:

'%
<.numDigits>>' % data

where data is either a single value or a tuple of values. This formatting system is described

at the end of

Chapter 3

.