hotspot3d
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Hi,
I am trying to run the demo code
hotspot3d uppro --measure average --output-dir prep/ --pdb pdb/ --gene-file demo.maf --parallel local --max-processes 6 1>demo.uppro.out 2>demo.uppro.err
and it gave the error:
HotSpot3D::HugoGeneMethods::makeHugoGeneObjects ERROR: no data from url request.
Any ideas how to fix this?
Thanks
hi, YonkoBigMom.
I have same problem too. Do you have fix it ?
Thx
It is caused by an outdated HUGO URL. I put a pull request (#25) on this.
More than a year has passed since this issue was opened and it appears that the outdated URL is still preventing the command hotspot3d uppro
from running. @JohnMCMa made a pull request on this topic and presumably solved the issue. However, I am now getting the very same error message with his forked HotSpot3D version:
HotSpot3D::HugoGeneMethods::makeHugoGeneObjects ERROR: no data from url request. Installing Mozilla::CA might fix this issue
.
Looks like the updated URL is also now outdated too. Because this issue significantly limits the usability of the HotSpot3D, I would be more than grateful if the authors would note this long-term problem and update the valid URLs to source code.
I believe editing the file /home/user/perl5/lib/perl5/TGI/Mutpro/Preprocess/HugoGeneMethods.pm may fix it? I replaced this line: #my $HugoUrl = "https://www.genenames.org/cgi-bin/hgnc_downloads?". with this line my $HugoUrl = "https://www.genenames.org/cgi-bin/download/custom?".
I believe editing the file /home/user/perl5/lib/perl5/TGI/Mutpro/Preprocess/HugoGeneMethods.pm may fix it? I replaced this line: #my $HugoUrl = "https://www.genenames.org/cgi-bin/hgnc_downloads?". with this line my $HugoUrl = "https://www.genenames.org/cgi-bin/download/custom?".
Also not work.