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huangyh09 / briekit

Preprocessing tool kit of BRIE project in splicing analysis
https://brie.readthedocs.io/en/latest/briekit.html
Apache License 2.0
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briekit-event-filter #1

Closed Ivymanman closed 5 years ago

Ivymanman commented 5 years ago

hi,I got this error when I run briekit-event-filter -a /path/to/A3SS.gff3.gz --anno_ref /path/to/gencode.vM22.annotation.gff3 -r /path/to/GRCm38.p6.genome.fa

5955 Skipped Exon events are input for quality check. 0 Skipped Exon events pass the qulity control. Traceback (most recent call last): File "xxxx/envs/briekit/bin/briekit-event-filter", line 10, in sys.exit(main()) File "xxxx/miniconda2/envs/briekit/lib/python2.7/site-packages/briekit/events/event_filter.py", line 395, in main g_idx, g_chr, g_start, g_stop = get_gene_idx(anno_out) File "xxx/miniconda2/envs/briekit/lib/python2.7/site-packages/briekit/events/event_filter.py", line 41, in get_gene_idx g_idx.append([now_g, last_g]) UnboundLocalError: local variable 'last_g' referenced before assignment

huangyh09 commented 5 years ago

Hi, the briekit-event-filter is only for the skipping exon events. You may need to define your own filters for the A3SS (alternative 3' splice site) event, which we haven't looked into.

Ivymanman commented 5 years ago

Thanks a lot 😅发自我的iPhone------------------ Original ------------------From: Yuanhua Huang notifications@github.comDate: Sat,Aug 3,2019 4:57 PMTo: huangyh09/briekit briekit@noreply.github.comCc: Ivymanman ncuskxiaolixing@163.com, Author author@noreply.github.comSubject: Re: [huangyh09/briekit] briekit-event-filter (#1)Hi, the briekit-event-filter is only for the skipping exon events. You may need to define your own filters for the A3SS (alternative 3' splice site) event, which we haven't looked into.

—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or mute the thread. [ { "@context": "http://schema.org", "@type": "EmailMessage", "potentialAction": { "@type": "ViewAction", "target": "https://github.com/huangyh09/briekit/issues/1?email_source=notifications\u0026email_token=AL6XVIFE2OEZVMLH7FUU2ZDQCVCBDA5CNFSM4IJCMSQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3PKLNI#issuecomment-517907893", "url": "https://github.com/huangyh09/briekit/issues/1?email_source=notifications\u0026email_token=AL6XVIFE2OEZVMLH7FUU2ZDQCVCBDA5CNFSM4IJCMSQKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3PKLNI#issuecomment-517907893", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { "@type": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

jihongma1010 commented 4 years ago

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...

Could you help me? Thanks