search

hanfang / Topsorter

Graphical assessment of structrial variants using 10x genomics data
10 stars 2 forks source link

vcf writer issue #11

Closed sridhar0605 closed 7 years ago

sridhar0605 commented 7 years ago

error 1: python topsorter.py -i large_svs.vcf [status] Topsorter started at 2017-05-15 17:29:19.555427 [status] Reading the vcf file: large_svs.vcf Traceback (most recent call last): File "topsorter.py", line 491, in worker.readVcf() File "topsorter.py", line 81, in readVcf with open(fn, 'r') as f: IOError: [Errno 2] No such file or directory: '/seq/schatz/hfang/Develop/Topsorter/data/grch38.chrom.sizes.txt'

fixed gave current path

error2: python topsorter.py -i large_svs.vcf [status] Topsorter started at 2017-05-15 17:36:36.966442 [status] Reading the vcf file: large_svs.vcf [execute] Exporting the large SVs to vcf and flanking regions to a bed file Traceback (most recent call last): File "topsorter.py", line 494, in worker.exportVcfBed() File "topsorter.py", line 107, in exportVcfBed vcf_writer.write_record(record) UnboundLocalError: local variable 'vcf_writer' referenced before assignment

hanfang commented 7 years ago

Hi there,

Thanks for this. I should have some bandwidth to look into this in ~3 weeks. Thanks.

Han

sridhar0605 commented 7 years ago

Hello team,

Did you get some time to look at this?

Thanks,