intersect1D "UnboundLocalError: local variable 'Aannots' referenced before assignment" error triggered by Inter-chromosomal interactions

[SplitInf]

Hi,

Thanks for making the tool available to the community. I noticed a bug when running intersect1D when the -b file contains a target that intersects with a inter-chrom interaction event. A workaround I noticed was if you add a dummy intra-chrom interaction into -a and -b file this error wouldn't be triggered. [pgltools 2.2.0]

• intra-chrom interactions only bedpe

  cat toy1.bedpe 
  chr1    710000  715000  chr1    935000  940000  
  chr1    825000  830000  chr1    935000  940000

• intra and inter chrom interactions bedpe

  cat toy2.bedpe 
  chr1    710000  715000  chr1    935000  940000  
  chr1    825000  830000  chr1    935000  940000
  chr1    920000  925000  chr2    935000  940000

• bed region corresponds to intra-chrom region

  cat targ1.bed 
  chr1    935000  940000
  chr2    935000  940000

• bed region corresponds to inter-chrom region

  cat targ2.bed 
  chr2    935000  940000

• intersect intra-chrom with intra-chrom only file -> works

  pgltools intersect1D -a toy1.bedpe -b targ1.bed -wa
  chr1    710000  715000  chr1    935000  940000  B   
  chr1    825000  830000  chr1    935000  940000  B   

• intersect intra-chrom target with intra and inter chrom file -> works

  pgltools intersect1D -a toy2.bedpe -b targ1.bed -wa
  chr1    710000  715000  chr1    935000  940000  B   
  chr1    825000  830000  chr1    935000  940000  B   
  chr1    920000  925000  chr2    935000  940000  B   

• intersect inter-chrom target with intra and inter chrom file -> error

  pgltools intersect1D -a toy2.bedpe -b targ2.bed -wa
  Traceback (most recent call last):
  File "intersect1D.py", line 403, in <module>
  intersect1D(A,B,args,header,headerB)
  File "intersect1D.py", line 272, in intersect1D
  res=_overlap1D(A,B,args['bA'],args['allA'],args['wa'],args['d'],args['v'],args['wb'],args['u'])
  File "intersect1D.py", line 258, in _overlap1D
  newPeaks.append([[chr1,start1,end1,chr2,start2,end2,"B"],Aannots])
  UnboundLocalError: local variable 'Aannots' referenced before assignment

[SplitInf]

i̶s̶s̶u̶e̶s̶ ̶r̶e̶s̶o̶l̶v̶e̶d̶ ̶w̶i̶t̶h̶ ̶f̶o̶r̶m̶a̶t̶b̶e̶d̶p̶e̶

[SplitInf]

Nope, problem persisted. It's not because of sorting.

[billgreenwald]

Hey I am getting around to responding to some of these, apologies for it being so long. Still having an issue/using the tool?

[auberginekenobi]

Hi Bill, Yep, just encountered the same problem with the same use case.

[SplitInf]

Hi Bill, yes this is still a problem. Sorry for the poorly worded description, but the examples should help.

[SplitInf]

erkk, sorry closed ticket by mistake.

[billgreenwald]

Should be fixed in 5662fa4e0c85702e6a1247a662cfaedb473f9965, try pulling and running

[billgreenwald]

This is also added as an explicit test case in the above push, and is pulled in to the 3.0.0 update, so this shouldnt be a problem. If any other behaviors come up let me know since its now easy to just add more tests.

If one of the original commenters can confirm it now works for them, please close when you comment back :)

[SplitInf]

seems to work now! thank you