Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

Method

Description

Example

append(data1,

data2, dtype)

Add one or more values on

the end of an array to make a

longer array. Unless an axis

is specified the result will be

a = array([[1, 2, 3],

[4, 5,

6]])


b = append(a, [7,8,9])


a flattened, 1D array. If an

axis is specified the array

added must have the same

number of dimensions, and

naturally must match the

shape along that axis. Note it

will generally be quicker to

use empty() and then fill

array values by index rather

than call append() multiple

times.

# Makes flat 1 x 9 array



c = append(a, [[7,8,9]],

axis=0)


# Makes 3 x 3 array

d = append(a, [[4],[7]],

axis=1)

# Makes 2 x 4 array

arange(start,

end, step, dtype)

Generates an array of equally

spaced numbers, from a start

point, up to (but not

including) an end point using

a given step size. The start

defaults to zero and the step

to 1. The data type will be

inferred from the arguments

unless specifically stated.

Similar to range/xrange in

standard Python, but for

more data types.

arange(3.0)

# Floats: array([0.0, 1.0,

2.0])

arange(7, 3, -1)



# Ints: array([7, 6, 5,

4])


arange(0, 6 ,2, float)

# Floats: array([0.0, 2.0,

4.0])

arange(3.2, 3.5, 0.1)



# Floats: array([3.2, 3.3,

3.4])


argmax(arry,

axis)

or

a.argmax(axis)



Gets an array of indices that

specify the position of the

maximum value in an array,

either along a specified axis

or in the flattened 1D version

of the array if no axis is

specified.

a = array([[1,2,8],

[9,1,1]])

argmax(a) # 3

# Position of max in 1D

argmax(a, axis=0)

# array([1, 0, 0])

# Which row has max for

each col

a.argmax(axis=1)

# array([2, 0])

# Which col has max for

each row

argmin(arry,



axis)

or

a.argmax(axis)



As above, but finds the

indices for the minimum

value. Also an inbuilt

method of numpy.array.

a = array([[1,2,8],

[9,1,1]])

a.argmin(0) # axis=0

# array([0, 1, 1])

# Which row has min for

each col



argsort(arry,

axis)

or

a.argsort(axis)



Compares the values in an

array to generate an array of

their indices in value-sorted

order. If the axis is not

specified the result refers to a

flattened 1D version of the

array.

a = array([5,9,3,4,1,8])



sortIndices = a.argsort()

print(sortIndices)

# [4,2,3,0,5,1] – min val

at a[4]


print(a[sortIndices])

# [1,3,4,5,8,9]

argwhere(arry)

Finds the indices of the non-

zero (or true) elements of an

array. Unlike nonzero(), the

returned indices are grouped

by element, rather than by

axis.

a1 = array([[8, 0, 0],



[0,

0, 9]])


indices = argwhere(a1)

# array([[0, 0], [1, 2]])

# Positions of non-zero

elements


cov(data1,

data2)

Makes an array representing

the sample covariance matrix

for given array or array-like

data. Each data row is taken

to be a different variable, and

each data column represents

a separate data point/vector.

The covariance matrix

represents the correlations

between different pairs of

variables (data dimensions).

x = [0.0, 1.0, 2.0, 3.0]

y = [0.4, 2.2, 3.9, 5.8]

cov(x) # 1.666667

cov(y) # 5.342500

cov([x, y])

# array([[1.666667,

2.983333],

[2.983333, 5.342500]])

cross(arry1,

arry2)


The cross-product between

two vector arrays. The arrays

must be 2 or 3 dimensional.

For 3D arrays the result is a

vector array that is

perpendicular to both input

vectors (where possible). For

2D arrays the result is the

determinant of the associated

2×2 matrix.

cross([0,1,0], [0,0,1])

# array([1, 0, 0])

cross((3,1),(1,2))

# 5


dot(arry1,

arry2)


or

a.dot(arry)

The dot product or scalar

product between two arrays.

For 2D matrices the result is

matrix multiplication. For

1D vectors the result is a

scalar, equivalent to the

m1 = array([[ 1, 2],

[-2,


0]])

m2 = array([[-1, 1],

[2,

3]])



magnitude of the projection

of one vector on to the other.

m3 = dot(m1, m2)

# array([[ 3, 7],

# [ 2, -2]])

v1 = array([1,2,3,4])

v1.dot(array([4,3,2,1])) #

20

dstack(arrays)



Combines a sequence (e.g.

list) of arrays into a larger

array by stacking them

depth-wise, along their third

axis. For example, combines

separate 2D matrices into a

3D tensor.

m1 = array([[1,2,3],

[4,5,6]])

m2 = array([[7,8,9],

[0,1,2]])

m3 = dstack([m1, m2])

# array([[[1, 7],[2, 8],

[3, 9]],


[[4,

0],[5, 1],[6, 2]]])

print(m3.shape)

# (2, 3, 2)

empty(sizes,

dtype)

Generates a new empty

array, of specified size. The

array will actually be filled

with arbitrary (but small)

numbers, rather than zero.

The data type may be

specified, but otherwise

defaults to floating point.

The size can be an integer or

a tuple of integers, one for

each axis, specifying number

of rows, columns etc.

a = empty((2,1))

# 2 x 1 array,

arbitrarily:

# array([[ 1.34634549e-

316],


# [

1.81895505e-317]])

eye(nRows,

nCols)

Creates an identity matrix of

a specified size; a 2D array

with ones on the diagonal

and zeros elsewhere. If the

number of columns is not

specified the matrix is

square.


eye(3)

# array([[ 1.0, 0.0, 0.0],

# [ 0.0,

1.0, 0.0],

# [ 0.0,

0.0, 1.0]])

histogram(arry,


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