Reference sequence doesn't exist error after following example

[kuanlinhuang]

I followed the example code to download hg19 but still get the reference sequence doesn't exist error. $ transvar config --download_anno --refversion hg19 $ transvar config --download_ref --refversion hg19 $ transvar panno -i 'PIK3CA:p.E545K' --ucsc --ccds Reference sequence doesn't exist samtools faidx file doesn't exist for reference Traceback (most recent call last): File "/usr/local/bin/transvar", line 30, in args.func(args) File "/usr/local/lib/python2.7/site-packages/transvar/anno.py", line 178, in main db = AnnoDB(args, config) File "/usr/local/lib/python2.7/site-packages/transvar/annodb.py", line 49, in init faidx.init_refgenome(args.reference if args.reference else None) File "/usr/local/lib/python2.7/site-packages/transvar/faidx.py", line 93, in init_refgenome refgenome = RefGenome(r) if r else None File "/usr/local/lib/python2.7/site-packages/transvar/faidx.py", line 22, in init self.load_faidx() File "/usr/local/lib/python2.7/site-packages/transvar/faidx.py", line 33, in load_faidx for line in self.faidx_handle: AttributeError: RefGenome instance has no attribute 'faidx_handle'

[zwdzwd]

Hi, sorry to see this trouble. If you give "transvar current" what is the output? is the file in the reference slot accessible?

[kuanlinhuang]

Thank you for the quick reply. Here it is; it's not available: $ transvar current reference version: hg19 reference: /Users/khuang/.transvar.download/hg19.fa Available databases: refseq: /Users/khuang/.transvar.download/hg19.refseq.gff.gz.transvardb ccds: /Users/khuang/.transvar.download/hg19.ccds.txt.transvardb ensembl: /Users/khuang/.transvar.download/hg19.ensembl.gtf.gz.transvardb gencode: /Users/khuang/.transvar.download/hg19.gencode.gtf.gz.transvardb ucsc: /Users/khuang/.transvar.download/hg19.ucsc.txt.gz.transvardb aceview: /Users/khuang/.transvar.download/hg19.aceview.gff.gz.transvardb known_gene: /Users/khuang/.transvar.download/hg19.knowngene.gz.transvardb

$ ls /Users/khuang/.transvar.download/hg19.fa ls: /Users/khuang/.transvar.download/hg19.fa: No such file or directory $ ll /Users/khuang/.transvar.download/hg19.refseq.gff.gz.transvardb ls: /Users/khuang/.transvar.download/hg19.refseq.gff.gz.transvardb: No such file or directory

[zwdzwd]

It turned out to be an issue after recent accommodation of python 3. The downloading wasn't properly finished. I just uploaded a fix. You should be able to get it through "pip install -U transvar" if you installed through pip

I have tested it on my end. Previously I didn't catch it due to a fall-back downloading that relies on HTTP-requests. Let me know if this fixed problem on your end.

Thanks for the feedback!

[kuanlinhuang]

Yes that worked. Thank you zwdzwd!