Python Programming for Biology: Bioinformatics and Beyond

6

Files

Contents

Computer files

File formats

Reading files

Using ‘

open

’

Reading lines of data

Working with variable file names

File reading examples

Reading whitespace-separated files

Reading FASTA files

Reading PDB files

Reading XML files

Reading PubMed XML files

Writing files

Example FASTA format writer

Column-delimited formats

Further considerations

File operations with the standard library

Pickling data

Computer files

A computer file is a means by which data is stored on a permanent basis, or at least until it

is deleted. It is held in a place such as a hard disk drive or removable storage device that is

separate from the active, temporary memory of a computer. While the active memory may

hold the current program and an amount of data, files represent a larger archive of stored

data  and  the  general  idea  is  that  this  should  survive  when  the  computer  is  switched  off.

Parts of this saved data may be copied into the active memory as required. Loading data

from files (which may be stored locally or transmitted via a network) places data into the

active memory so that it can be worked upon efficiently. This data might be the code for a

computer  program  which  can  then  be  executed  to  do  a  job.  Naturally  we  save  program

instruction code as a file so that it may be used as many times as desired, without having

---

to rewrite anything.

This chapter will focus on data files that store information for programs to work with,

rather than the program files themselves, given that we can trust the Python interpreter to

handle the loading and running of Python code. We will show how data can be read into a

program and written out from a program, e.g. to and from files stored on disk. Such data

files  come  in  a  large  variety  of  shapes,  sizes  and  forms  (unlike  Python  files,  which

conform to a single, precise standard). Information can be stored in an endless number of

ways,  sometimes  at  the  whim  of  the  programmer,  but  fortunately  in  the  spirit  of

cooperation (including mutual financial interest) particular types of data are often stored in

a standardised way, with a known specification.

Stored data is represented as a series of binary numbers, i.e. zeros and ones (merely the

absence  or  presence  of  a  signal)  and  a  connected  series  of  data  that  goes  together,  as  a

named  unit,  is  what  we  mean  by  a  file.  However,  there  are  two  distinct  types  of  file:

binary  and  plain  text.  The  difference  between  these  is  that  plain  text  files  only  use  a

limited series of binary codes to describe data as character symbols, like digits and letters.

Binary  files  are  not  restricted  in  this  sense,  but  their  interpretation  is  dependent  upon

having the right kind of computer system and/or program to load them. Plain text files are

much  more  universal  and  keep  to  a  standard  set  of  binary  codes,  so  that  they  will  be

interpretable in the same way whatever the computer system or programming language. In

this chapter we concentrate on data stored as plain text files, and this will cover most of

the file standards used in biology.