Hello, I have created a script that successfully searches for keywords (specified by user) within a Blastx output file in XML format. Now, I need to write those records (query, hit, score, evalue, etc) that contain the keyword in the alignment title to a new file. I have created separate lists for each of the query titles, hit title, e-value and alignment lengths but cannot seem to write them to a new file. Problem #1: what if Python errors, and one of the lists is missing a value...? Then all the other lists will be giving wrong information in reference to the query ("line slippage", if you will...). Problem #2: even if Python doesn't error, and all the lists are the same length, how can I write them to a file so that the first item in each list is associated with each other (and thus, item #10 from each list is also associated?) Should I create a dictionary instead? Problem#3: dictionaries have only a single value for a key, what if my query has several different hits? Not sure if it will be overwritten or skipped, or if it will just error. Any suggestions? My current script:
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
import re
#obtain full path to blast output file (*.xml)
outfile = input("Full path to Blast output file (XML format only): ")
#obtain string to search for
search_string = input("String to search for: ")
#open the output file
result_handle = open(outfile)
#parse the blast record
blast_records = NCBIXML.parse(result_handle)
...