Python Programming for Biology: Bioinformatics and Beyond

Obtaining sequences with BioPython

If you wish to use any of the above examples in a real situation you will naturally want to

get  your  sequences  from  a  database  or  file  where  they  are  stored,  rather  than  having  to

type sequence letters into a Python file. With a working knowledge of Python you would

hopefully  be  able  to  extract  sequence  information  from  the  various  text  file  formats.

However,  for  the  most  part  this  is  a  solved  problem  and  in  many  instances  you  can  rely

upon existing modules to extract sequences from files or databases. A good source of such

modules  is  the  BioPython  library,  and  below  we  illustrate  how  to  use  BioPython  to  get

sequence  data  from  a  few  common  sources.  These  examples  assume  that  BioPython  is

installed  correctly  on  your  system  and  available  to  Python  as  the  Bio  module.  See

http://www.cambridge.org/pythonforbiology

for links to download BioPython.