huangyh09
commented
4 years ago Hi,
I'm not very sure what causes this issue. There are two possibilities:
1) the format of Gencodev32_hg38_ercc_refseq.gtf is not compartible. The required format is here: http://diceseq.sourceforge.net/manual.html#annotation-format
2) not sure if you are using Python 2.7, as Python 3 is not compatible.
Let me know if it is any of them. Yuanhua
hi, I got this error when I run briekit-event -a /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf -o /disk2/brie_rnasplicing_bc25/bc25_as/ Making GFF alternative events annotation... Input annotation files: /disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf Output dir: /disk2/brie_rnasplicing_bc25/bc25_as/ ('Reading table', '/disk1/reference_genome/hg38_ucsc_ercc/Gencodev32_hg38_ercc_refseq.gtf') Traceback (most recent call last): File "/home/JHma/miniconda3/envs/RNASEQ/bin/briekit-event", line 11, in load_entry_point('briekit==0.2.2', 'console_scripts', 'briekit-event')() File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 175, in main File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 69, in defineAllSplicing File "build/bdist.linux-x86_64/egg/briekit/events/event_maker.py", line 39, in prepareSplicegraph File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 85, in populateSplicegraph File "build/bdist.linux-x86_64/egg/briekit/events/parseTables.py", line 64, in readTable_gff UnboundLocalError: local variable 'exons' referenced before assignment Could you help me? Thanks