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zwdzwd / transvar

TransVar - multiway annotator for precision medicine
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Bug in annotation download code? #43

Closed adfnih closed 3 years ago

adfnih commented 4 years ago

Good afternoon,

When I try to download the annotations for hg19 as shown in the first example in the quick start documentation, I get a series of file access errors:

% transvar config --download_anno --refversion hg19 [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.refseq.gff.gz.transvardb or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.refseq.gff.gz.transvardb.gene_idx or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.refseq.gff.gz.transvardb.trxn_idx or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.refseq.gff.gz.transvardb.loc_idx or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.refseq.gff.gz.transvardb.loc_idx.tbi or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.ccds.txt.transvardb or target directory not found [_download_] warning: file not available: http://zwdzwd.io/transvar_user/annotations/hg19.ccds.txt.transvardb.gene_idx or target directory not found (many other lines are deleted)

I think that there is a bug in the code that is generating the filenames for download, because if I strip off the transvardb suffixes, the downloads work in my web browser. Is this a known problem, and are there any plans to fix it?

Thanks, Andy

cangfengzhe commented 3 years ago

I have the same problem

BunnyBoss commented 3 years ago

Same problem..Any possible solution ??? But, For me downloads are not working in web browser too.

glormph commented 3 years ago

Can't download here either (annotations and reference assembly). The config.py file contains the line

dwroot = 'http://zwdzwd.io/transvar_user/annotations/'

which seems to be where the script downloads annotations and reference assembly. But that website seems to not host anything at the moment. I'm hoping the data have moved and only a small edit in the code will suffice for this.

zwdzwd commented 3 years ago

Sorry for the late response. This should just be fixed in version 2.5.10.20211024. Btw, the new host is at https://zhouserver.research.chop.edu/TransVar/annotations/