Python Programming for Biology: Bioinformatics and Beyond

2

http://cython.org

.

3

Although we don’t go further than this here, that natural next step would be to distribute

jobs over many separate computers.

4

http://openmp.org

.

5

Dependent on what kind of CPU is present.

6

Python float numbers have this double precision as standard.

7

 It  will  be  compiled  so  that  it  runs  on  a  particular  processor  architecture,  such  as  x86,

x86-64, ARM etc.

8

The count of 10 includes the newline character, ‘\n’.

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Appendices

---

These  appendices  contain  simple  explanations  and  definitions  for  a  subset  of  the  Python

language,  its  standard  libraries  and  a  few  of  the  key  modules  used  in  this  book.  The

objective is not to give a complete description of every possible option, which is already

documented (and will be more up-to-date) on the Internet. Rather, the aim is to cover all of

the components used in this book as well as a few extra useful details in relatively plain

English, to help with learning the language. Hence, it is deliberate that we have simplified

or  omitted  certain  details  to  avoid  obfuscating  the  main  points  for  novice  programmers.

While  we  describe  most  of  the  core  components  of  standard  Python,  for  some  of  the

libraries  we  will  only  highlight  some  parts  we  have  found  particularly  useful.  In  some

cases, where we don’t describe individual components, we will describe what a library or

a module is generally used for, in order to guide further investigation.

In

addition

to

the

material

presented

here,

the

website

http://www.cambridge.org/pythonforbiology

provides

links

to

full,

in-depth

documentation for Python and the associated libraries that are used throughout this book.

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