Parsing A Uniprot Flat File

Question

[Deepu]

Can anybody please let me know or help with parsing a uniprot flat file and access the information in the annotation (FT) line and produce an output file in python script. FT line is the one in a general uniprot flat file describing the nature of the proteins. Script written to this must produce an output file with the information in this line.

[Pierre Lindenbaum]

homework ? what did you try so far ?

[Jarretinha]

Can you use Biopython?

[Deepu]

I think we can use biopython. Its not homework but part of project.

[Michael Schubert]

Please don't forget to accept one of the answers below, the problem appears to be solved.

Answer 1

[Chris]

With BioPython, the task to access the feature information is very simple:

from Bio import SwissProt
for record in SwissProt.parse(open('/path/to/your/uniprot_sprot.dat')):
  for feature in record.features:
    print feature

How to save that into a file is also very simple.

Chris

Answer 2

[Neilfws]

If you can use BioPython, see Chapter 9: Swiss-Prot and ExPASy in the tutorial.

Alternative quick and dirty approach:

grep ^FT myfile.dat

Although that will not deal well with feature descriptions that span several lines.