[Tutor] List of Lists for three Frames

ani fantasticfaces2 at gmail.com
Sat May 17 09:01:17 CEST 2014


So I thought it would be cool to read a sequence at three different frames, 
which I have pasted below. However, I've come across a conundrum: how to 
make a list of lists. See, I'd like a final output that displays data of the 
type of frame with a + or a - to signify the direction of the read (+1,+2, 
+3, -1, -2, -3), the numerical position of each start codon along with its 
stop codon, and the length between the start and stop codons. (I am only 
looking for the longest ORFs) An example of the output would look like this:

 +1 57166..61908  4743. 
The reason why I'd like a list of lists is so that I can take all the Starts 
I found in the code below, store it, then be able to place it in to the 
output somehow. I thought that maybe a list of lists would be the best way 
of getting this information from three different frames. However, I'm not 
sure how to go about this... could someone give me a way to start? The while 
loops work fine, last time I checked. Thanks.

def codons(self, frame_one, frame_two, frame_three): 
    while frame_one <=len(self.seq): 
        yield (self.seq[frame_one:frame_one+3]) 
        frame_one += 3

    while frame_two <=len(self.seq):
        yield (self.seq[frame_two:frame_two+3])
        frame_two += 3

    while frame_three <=len(self.seq):
        yield (self.seq[frame_three:frame_three+3])
        frame_three += 3

val = seq.codons(0,1,2)

for i in val:
    return(i)

self.startlist.append[[frame_one], [frame_two], [frame_three]]



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