I am using Breakseq to find mechanism of structure variations (SV) mapped using different package. I got stuck while using svMech module, probably due to lack of its user manual.
I only want to find mechanism of SV, so I have commented Ancestral state and feature analysis in annotate script under bin directory of breakseq.
It is working fine if I give only deletions in gff file. But when I give Insertions in gff file, it exits with following error
********** Creating standard breakpoint library **********
Traceback (most recent call last):
File "/home/pankaj/breakseq/breakseq-1.3/bin/svUtil/svStd.py", line 20, in <module>
File "/home/pankaj/breakseq/breakseq-1.3/lib/biopy/io/SV.py", line 103, in get_sequence
return self.base.get_sequence(self.name, self.start, self.end)
AttributeError: ‘NoneType’ object has no attribute ‘get_sequence’
Command exited with non-zero status 1
0.13user 0.04system 0:00.21elapsed 83%CPU (0avgtext+0avgdata 60800maxresident)k
0inputs+8outputs (0major+4306minor)pagefaults 0swaps
Could you please resolve my following queries regarding breakseq
(1) For Insertion, Do I need to provide inserted sequence explicitly or does this package find internally.
(2) Does this package also find mechanism of translocations. If yes, which keyword should I use in 3rd column of gff file.
1) you have to provide the inserted sequence. (see http://sv.gersteinlab.org/breakseq/ as an example)
2) it does not currently support translocations. (not mentioned on our paper)