[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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