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 # wild_aa = sys.argv # position = sys.arg # mutant_aa = sys.arg #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