How Do I Loop Over Sequences With Biopython?

Question

[T]

Hi,

I'm new to biopython. I can't seem to get nested for loops to iterate properly. Here's a simple example:

from Bio import SeqIO

infile = file('testseq.fna')

midfile = file('mids.fna')

c = 0


for midseq,line in SeqIO.parse(midfile,"fasta"):
    print midseq.id
    print midseq.seq
    for line in SeqIO.parse(infile,"fasta"):
        print line.seq

I have 12 simple fasta records in testseq.fna, and 96 mid identifiers in mids.fna. I should get a list of 96 mid ids and seqs, each followed by 12 testseq sequences, but what I get is just the first mid and sequences then just the other mids with no sequence... run it and you will see what I mean. I'm pulling my hair out - why doesn't Python run the 'line' loop for each 'mid' loop like it should??

Thanks for any help - I know its surprising but I couldn't find an answer to this anywhere (on python forum they were just rude!).

Theo

Answer 1

[Istvan Albert]

Your stream reaches the end of the file by the end of the first iteration.

Move the line:

infile = file('testseq.fna')

Inside the loop like so:

for midseq,line in SeqIO.parse(midfile,"fasta"):
    infile = file('testseq.fna')

Answer 2

[T]

Brilliant! thanks. You have no idea how long that has taken to find out! I still don't know why it works though.

Is it that opening the file again for each primary loop resets the iteration? I can't find anywhere in a Python manual where it says you have to do that! If it was a list and not a file would it have to be defined in the loop like that too?

Thanks again,

Theo

[Istvan Albert]

when you open a file you open a stream to it, once that runs out you would either need to go back to the beginning with a seek operation or just open the file in a new stream. Each time you open the file it is an entirely new stream to the same content - you can be in different locations of the same file if you open it in different streams.

[Weronika]

Essentially what's going on here is that a file acts more like an iterator than like a list. Try running through an iterator (made by something like iterator = iter([1,2,3])) in a loop multiple times(like for i in range(3): for x in iterator: print x, and you'll see that it only runs through the 1,2,3 items in the first inner for loop, and acts as empty after that - unlike a list, which would act the same in every inner for loop. But you're right, the python manual isn't very explicit about that.