Question

I would like to build up a list using a for loop and am trying to use a slice notation. My desired output would be a list with the structure:

known_result[i] = (record.query_id, (align.title, align.title,align.title....))

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

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

which results in:

list assignment index out of range. 

I am iterating through a series of sequences using BioPython’s NCBIXML module but the problem is adding to the list. Does anyone have an idea on how to build up the desired list either by changing the use of the slice or through another method?

thanks zach cp

(crossposted at [Biostar])1

Answer 1

You cannot assign a value to a list at an index that doesn’t exist. The way to add an element (at the end of the list, which is the common use case) is to use the .append method of the list.

In your case, the lines

known_results[i] = record.query_id     
known_results[i][1] = (align.title for align in record.alignment)

Should probably be changed to

element=(record.query_id, tuple(align.title for align in record.alignment))
known_results.append(element)

Warning: The code above is untested, so might contain bugs. But the idea behind it should work.