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immunogenomics / goshifter

GoShifter
http://www.broadinstitute.org/mpg/goshifter/
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Error in running given example #2

Open avinoamshye opened 7 years ago

avinoamshye commented 7 years ago

Running the example as given with proxy files created with ProxyFinder, I got the following error:

Traceback (most recent call last): File "./goshifter.py", line 187, in args['--proxies']) File "/specific/netapp5_2/elkon/avinoamshye/goshifter/functions.py", line 109, in enrichPermRandBoundryPeakShift_tabixLd snpPeakInfo, ldsnpPeakInfo = permRandBoundryPeakShift(snpInfoChr,peaksTree,ldInfo,expand,minShift,maxShift,nPerm) File "/specific/netapp5_2/elkon/avinoamshye/goshifter/functions.py", line 304, in permRandBoundryPeakShift peaksToSnp = peaks2region(bounds,peaksTree,expand) File "/specific/netapp5_2/elkon/avinoamshye/goshifter/functions.py", line 425, in peaks2region maxbp = bounds[chrom][snp]['maxbp'] + expand TypeError: unsupported operand type(s) for +: 'dict' and 'float'

It appears only some of the boundary values are still enclosed in dictionaries of the form {'bp': ... } I could't find the reason for this so I added an if statement to extract the floats, assuming these values are the wanted ones. This seem to work without any more errors, but I'm not sure the values inside the occasional dictionaries are correct. I'd love to hear your thoughts on this.

erolaPC commented 6 years ago

Hello, I am having the same problem with proxy files created by ProxyFinder. Could you help me to solve it?

sckinta commented 5 years ago

Hello, I still have the same problem after pull the most updated commit. Could you help?

Traceback (most recent call last):
  File "./goshifter.py", line 187, in <module>
    args['--proxies'])
  File "/mnt/isilon/sfgi/programs/goshifter/functions.py", line 107, in enrichPermRandBoundryPeakShift_tabixLd
    snpPeakInfo, ldsnpPeakInfo = permRandBoundryPeakShift(snpInfoChr,peaksTree,ldInfo,expand,minShift,maxShift,nPerm)
  File "/mnt/isilon/sfgi/programs/goshifter/functions.py", line 301, in permRandBoundryPeakShift
    peaksToSnp = peaks2region(bounds,peaksTree,expand)
  File "/mnt/isilon/sfgi/programs/goshifter/functions.py", line 426, in peaks2region
    minbp = bounds[chrom][snp]['minbp'] - expand
TypeError: unsupported operand type(s) for -: 'dict' and 'float'
Arya-bioinformatics commented 5 years ago

I have the same problems