Question: Bx-Python Question About Bed_Intersect_Basewise.Py
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Amit Indap • 60 wrote:
Sorry, Galaxy I hit sent by accident in my earlier message.
Like I said, I had a question about bed_intersect_basewise.py My first
bed file has the following interval:
chr22 267 572
and my second bed file has the intervals:
chr22 147 267
chr22 267 387
chr22 387 507
chr22 507 627
When I run the program, I get the answer
chr22 202 572
But I'm trying to see if there is a way I can get the complement,
bases in the second file that don't overlap the first. The desired
answer would be:
chr22 147 267
chr22 572 627
I know there is a -v option on bed_intersect.py, but I want the
equivalent basewise behavior. I was trying to poke around the
BinnedBitSet code, and I see there is an invert method, but calling
the invert method has some side effects on the rest of the code
(either the next_set or next_clear call), and I get a run-time error.
The BinnedBitSet code somewhat of a blackbox to me, but I'd appreciate
any pointers in the right direction.
Thanks for your help,
Amit Indap
--
Amit Indap
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modified 8.0 years ago
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James Taylor ♦ 470
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written
8.0 years ago by
Amit Indap • 60
