Parse Ncbixml Output Into A Python List Of Hits

Question

[Zach Powers]

I would like to parse an NCBIXML file to obtain a list if the format:

known_results[i]=(query title, (hit_name,hit_name,hit_name....))

However I am having trouble getting the slice operator to work:

    knowns = "output.xml" 
    i=0
    for record in NCBIXML.parse(open(knowns)): 
        print record.query_id
        known_results[i] = record.query_id     
        known_results[i][1] = (align.title for  align in i.record.alignment)     
        i+=1

which results in:

list assignment index out of range

since i can do known_results[1]= "sample text" I think the problem is that I cannot use the slice method with a variable.

Can anyone suggest and alternative way to create this list?

thanks zach cp

---

crossposted with answer at StackOverflowlink text

---

There are two good answers on stackoverflow. The first uses list.append(), the second uses dictionaries. THe major problem with my construct is that you cannot assign values to parts of a list that have yet to be created.

[Niek De Klein]

Is known_results a list, or a list of lists?

[Zach Powers]

its a list of lists. the answer on the best ways to do this is on the StackExchange link.

Answer 1

[Damian Kao]

It's probably better to use a dictionary in this case:

knowns = "output.xml" 
known_results = {}
for record in NCBIXML.parse(open(knowns)): 
   print record.query_id
   known_results[record.query_id] = [align.title for align in i.record.alignment]

Now if you want to access your data, you can:

for queryID, alignments in known_results.items():
    print queryID
    for alignment in alignments:
        DO STUFF WITH ALIGNMENT