how can I calculate the number of gaps in sequences:
s1='G _ A A T T C A G T T A'
s2='G G _ A _ T C _ G _ _ A'
s3='G A A T T C A G T _ T _'
her the number of
'_' is 8
I try the following:
for i in range(0, len(s1), 3):
for x,y,z in zip(s1,s2,s3):
if (x=='_') or (y=='_')or (z=='_') :
it gives 6 not 8
Your code returns 7 which is the total count of all the underscores minus the extra underscore in the third to last position. You can fix that by removing the or-test (which short-circuits the tests when a match is found).
Also note there is no need to triple-zip the code or to loop with a stride-of-three.
Here is a cleaned-up version of your original code:
def count(): gap=0 for x,y,z in zip(s1,s2,s3): if (x == '_'): # these if-stmts don't short-circuit gap += 1 if (y == '_'): gap += 1 if (z == '_'): gap += 1 return gap
There are other ways to do this faster (i.e. the str.count method) but I wanted to show you how to repair and clean-up your original logic. That ought to put you on the right track when you do other analytics.
Strings have a count() method:
s1.count('_') + s2.count('_') + s3.count('_')
_'s in the 10th position only get counted twice. You should get 7, rather than 6.
The simple solution is
sum([item.count('_') for item in [s1,s2,s3]])