Question: Problem With Intersect (Bx)
0
Ross Hardison • 270 wrote:
The intersection tool under "Operate on Genomic Intervals (bx)" is
not working for returning either overlapping regions or overlapping
pieces. The intersection and overlaps in the non-bx operations
section are working.
I was running intersection (bx) on a set of Mathieu Blanchette's
PReMods (118,402 regions) with our RP>0.05 intervals (314,040
regions), in hg17, requiring at least 10bp overlap. Here are the
error messages.
For returning overlapping pieces:
An error occurred running this job: Traceback (most recent call
last): File "./tools/new_operations/gops_intersect.py", line 63, in ?
main() File "./tools/new_operations/gops_intersect.py", line 56, in
main for line in intersect([g1,g2], pieces=pieces, mincols=mincols):
File "
For returning overlapping regions:
An error occurred running this job: Traceback (most recent call
last): File "./tools/new_operations/gops_intersect.py", line 63, in ?
main() File "./tools/new_operations/gops_intersect.py", line 56, in
main for line in intersect([g1,g2], pieces=pieces, mincols=mincols):
File "
I'll leave the files and results in my history for a while in case
that is helpful.
Thanks,
Ross
Ross Hardison
T. Ming Chu Professor of Biochemistry and Molecular Biology
The Pennsylvania State University
304 Wartik Laboratory
University Park, PA 16802
e-mail: rch8@psu.edu
phone: 814-863-0113 FAX: 814-863-7024