Ashley F wrote:
ok...here's the function I've written so far.
def padWithGaps(seq):
for letter in seq:
letter="-"
line=len(seq)
dashline=line*letter
return dashline
I don't think that's a useful function. It seems to do a HUGE amount of
work that just keeps getting thrown away. Let's say seq = "GACT", this
function will do the following:
letter = "G"
letter = "-"
line = 4 # len of seq
dashline = "----"
letter = "A"
letter = "-"
line = 4
dashline = "----"
letter = "C"
letter = "-"
line = 4
dashline = "----"
letter = "T"
letter = "-"
line = 4
dashline = "----"
It does everything four times. Now imagine that seq is a million
characters long instead of four! This will do the job *much* faster:
def padWithGaps(seq):
return "-" * len(seq)
*Much* faster, much easier to read.
[...]
I don't know what to do at the end of my loop but what I'm trying to do in
pseudocode is:
"if that alignment has the best score seen so far
save the score and the alignment
print the best score and the best alignment"
You need to store the current best score and the current best alignment.
Then each time around the innermost loop, you need to calculate the
score and alignment (as you already do), and compare them to the best
seen so far. If they are worse or equal, you don't need to do anything,
just go on to the next loop as normal. But if they are better, then you
need to update the best score and alignment, and print them.
if score > best_score:
best_score = score
best_alignment = alignment
print 'best seen so far is', score, alignment
Does that help? Try writing the code, and if you still can't get it
working, ask again.
--
Steven
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