Retrieving Swissprot FT details for a particular amino acid position using Python

Question

[a.gardner]

Hi,

I am new so my apologies if I phrase things incorrectly.

I am trying to extract information from a Swissprot file for a mutation. For example I need to know the Domain it is positioned in and the secondary structure.

The input variables are: acc_number (the swissprot accession code), wild_aa (wild amino acid), position (that is the number amino acid in the protein), mutant_aa (the replacement amino acid).

I have got as far as retrieving the features using

for feature in record.features:
    print feature

How do I extract the secondary structure information from this to determine whether my amino acid is in a strand, helix, turn or random coil (if no secondary structure is recorded then I would say none).

My full code to date is below...as you will guess I am a total beginner with Python and Biopython (in fact with programming!):

Thanks in advance

#!/usr/bin/env python

import time
import sys # this module provides access to the input variables
import os
from Bio import ExPASy # this will allow a Swiss-Prot file to be opened
                       # over the internet using the accession number.
from Bio import SwissProt #this will allow the file to be read.

# This section receives the parameters from user input via the website:
# This will be commented out during the development period and temp. 
# variables will be used.

# acc_number = sys.argv[1]
# wild_aa = sys.argv[2]
# position = sys.arg[3]
# mutant_aa = sys.arg[4]

#Temp variables for developing:

acc_number = 'P01308'
wild_aa = 'L'
position = '43'
mutant_aa = 'P'

# next step is to retrieve the text file from swissprot to parse.
# this uses the acc_number variable:
handle = ExPASy.get_sprot_raw(acc_number)

# this reads the swissprot file:
record = SwissProt.read(handle)

# test to see if record has been retrieved:
print record.description

# next section will parse the sequence information using the position variable
# will determine the secondary structure location of the mutation

#obtaining sequence and placing it in a variable.
sequence = record.sequence
#print sequence

# accssing the secondary structure and domain information from FT lines
for feature in record.features:
    print feature

# Check that the wild amino acid is correct

Answer 1

[Ram]

The documentation refers to features as a tuple with key name, start, from, description. To see how a record looks like in plain text, check this out: http://www.uniprot.org/uniprot/P01308.txt

I've never used Bio.SwissProt.Record before, but you should probably be able to get feature[0] where feature[1] <= position and feature[2] >= position

This is the logic, implementing it in Python should not be a problem.

References:

1. http://www.uniprot.org/uniprot/P01308.txt
2. http://biopython.org/DIST/docs/api/Bio.SwissProt.Record-class.html
3. http://www.tutorialspoint.com/python/python_tuples.htm

[a.gardner]

Thank you, it works (though I feel a total numpty!)

[janemanny]

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