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)
#initialize lists
query_list=[]
hit_list=[]
expect_list=[]
length_list=[]
#create 'for loop' that loops through each HIGH SCORING PAIR in each ALIGNMENT from each RECORD
for record in blast_records:
for alignment in record.alignments: #for description in record.descriptions???
for hsp in alignment.hsps: #for title in description.title???
#search for designated string
search = re.search(search_string, alignment.title)
#if search comes up with nothing, end
if search is None:
print ("Search string not found.")
break
#if search comes up with something, add it to a list of entries that match search string
else:
#option to include an 'exception' (if it finds keyword then DOES NOT add that entry to list)
if search is "trichomonas" or "entamoeba" or "arabidopsis":
print ("found exception.")
break
else:
query_list.append(record.query)
hit_list.append(alignment.title)
expect_list.append(expect_val)
length_list.append(length)
#explicitly convert 'variables' ['int' object or 'float'] to strings
length = str(alignment.length)
expect_val = str(hsp.expect)
#print ("\nquery name: " + record.query)
#print ("alignment title: " + alignment.title)
#print ("alignment length: " + length)
#print ("expect value: " + expect_val)
#print ("\n***Alignment***\n")
#print (hsp.query)
#print (hsp.match)
#print (hsp.sbjct + "\n\n")
if query_len is not hit_len is not expect_len is not length_len:
print ("list lengths don't match!")
break
else:
qrylen = len(query_list)
query_len = str(qrylen)
hitlen = len(hit_list)
hit_len = str(hitlen)
expectlen = len(expect_list)
expect_len = str(expectlen)
lengthlen = len(length_list)
length_len = str(lengthlen)
outpath = str(outfile)
#create new file
outfile = open("__Blast_Parse_Search.txt", "w")
outfile.write("File contains entries from [" + outpath + "] that contain [" + search_string + "]")
outfile.close
#write list to file
i = 0
list_len = int(query_len)
for i in range(0, list_len):
#append new file
outfile = open("__Blast_Parse_Search.txt", "a")
outfile.writelines(query_list + hit_list + expect_list + length_list)
i = i + 1
#write to disk, close file
outfile.flush()
outfile.close
print ("query list length " + query_len)
print ("hit list length " + hit_len)
print ("expect list length " + expect_len)
print ("length list length " + length_len + "\n\n")
print ("first record: " + query_list[0] + " " + hit_list[0] + " " + expect_list[0] + " " + length_list[0])
print ("last record: " + query_list[-1] + " " + hit_list[-1] + " " + expect_list[-1] + " " + length_list[-1])
print ("\nFinished.\n")
