Dear tutors:
this question is in continuation of my previous
question about list manipulations where Kent and Bob
helped me.
Thanks to you both.
My aim was to walk along coordinates of exon of a gene
on a chromosome. In simple terms:
Coordinates of a variable G1:
a1 : 3-8
b2 : 10-25
c3 : 7-18
d4 : 10-13
Now, since these coordinates are in ranges of others,
I can define the extreames of the variables, which are
3 and 25.
Example pictorially:
3-----8
10---------------25
7-------------18
10---13
Now, I have variables G1....Gn. Each variable may
have individual pieces a1(n),b2(n),c3(n).....z(n).
my kind of solution, which is very crappy (i assume):
Sort the list:
[3,8] [3,8]
[10,25] sort [7,18]
[7,18] --------> [10,13]
[10,13] [10,25]
I loop through each list and check if list[0] is in
range of previous list list[1] AND if it is less or
greater than. If less, I retain the greater number and
loop through.
The question to the forum is, I am using range()
function to solve this. Since the numbers in the
example are small, it worked. in the real world
example , it did not work, because computer slowed
down and eventually crashed. The range(81393417) is
really big.
question:
1. What to do If I have to check if a number is in
range of 81393417.
2. Is there any alternative.
3. is solution that I have, is it appropriate.
Please help.
My real world example:
kd ={'GeneID:1519':
['81393417\t81395369','81397635\t81397727','81398841\t81399004','81406661\t81406782','81408670\t81408837','81411616\t81411755','81412455\t81412563','81423012\t81423195'],
'GeneID:445347':['37788202\t37788789','37790730\t37790777','37793908\t37794237','37802146\t37802206''37788202\t37788789','37790730\t37790777','37793908\t37794237','37802146\t37802206']}
kk = ['GeneID:1519','GeneID:1519','GeneID:445347']
for i in kk:
if kd.has_key(i):
pairs = [map(int,x.split('\t'))for x
in kd[i]]
pairs.sort()
i = iter(pairs)
last = i.next()
for cur in pairs:
if cur[0] in range(last[1]):
if cur[1] > last[1]:
last =
[last[0],cur[1]]
else:
last =
[last[0],last[1]]
else:
print last
cur = last
print last
Thanks
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