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realbigws / RaptorX_Property_Fast

RaptorX-Property: a Standalone Package for Protein Structure Property Prediction
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Hardcoded path in run_raptorx-ss8.pl #7

Closed miguelcorrea closed 5 years ago

miguelcorrea commented 5 years ago

Hi,

In line 3 of run_raptorx-ss8.pl RaptorX-Property is assumed to be in the home directory: $raptorx=$ENV{"HOME"}."/RaptorX_Property_Fast"; If it's not (e.g. in a network filesystem) this will make it crash with the error "Failed to generate TGT file". This might be related to issue #6.

realbigws commented 5 years ago

Hi, Miguel.

I agree with you.

Now that the RaptorX_Property_Fast is obsoleted. Please try the new version below: https://github.com/realbigws/Predict_Property

In this new version, all the path issues have been solved. Also, I separate the feature generation module to TGT_Package: https://github.com/realbigws/TGT_Package

Please try it and let me know.

Best, -Sheng

On Mon, May 6, 2019 at 8:04 AM Miguel Correa notifications@github.com wrote:

Hi,

In line 3 of run_raptorx-ss8.pl RaptorX-Property is assumed to be in the home directory: $raptorx=$ENV{"HOME"}."/RaptorX_Property_Fast"; If it's not (e.g. in a network filesystem) this will make it crash with the error "Failed to generate TGT file". This might be related to issue #6 https://github.com/realbigws/RaptorX_Property_Fast/issues/6.

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miguelcorrea commented 5 years ago

Hi Sheng,

Thanks for the heads-up. I think it would be good to have a deprecation warning and a link to the new version in the README and the scripts. I've already run RaptorX_Property_Fast for about 1000 sequences; should I expect changes in predictions in the new version? I'm mainly interested in predicting secondary structure and solvent accessibility.

Best, Miguel

realbigws commented 5 years ago

On Mon, May 6, 2019 at 12:14 PM Miguel Correa notifications@github.com wrote:

Hi Sheng,

Thanks for the heads-up. I think it would be good to have a deprecation warning and a link to the new version in the README and the scripts. I've already run RaptorX_Property_Fast for about 1000 sequences; should I expect changes in predictions in the new version? I'm mainly interested in predicting secondary structure and solvent accessibility.

If you're using the same protocol to generate the TGT file with the same database (by default, it should be uniprot20_2016_02), then you shall obtain exactly the same result between RaptorX_Property_Fast and Predict_Property.

Thanks for your kind suggestion. I've added a WARNING message in the README file of the RaptorX_Property_Fast package.

Best, -Sheng

Best, Miguel

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miguelcorrea commented 5 years ago

Thanks! With this we can close this issue.