从blastx输出文件中提取特定条目，写入新文件

Question

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") 

Answer 1

If I understand your problem correctly you could use a default value for the line slippage thing like:

try:
  x(list)
except exception:
  append_default_value(list)

http://docs.python.org/tutorial/errors.html#handling-exceptions

or use tuples for dictionary keys like (0,1,1) and use the get method for your default value.

http://docs.python.org/py3k/library/stdtypes.html#mapping-types-dict

If you need to maintain data structures in your output files you might try using shelve:

or you could append some type of reference after each record and give each record a unique id for example ' #32{somekey:value}#21#22#44# '

again you can have multiple keys using a tuple.

I don't know if that helps, you might clarify exactly what parts of your code you have trouble with. Like x() gives me output y but I expect z .