wglab/phenolyzer

phenotype-based prioritization of candidate genes for human diseases

phenolyzer's Issues

something wrong using phenolyzer website

Sorry to bother you.But someting goes wrong when using phenolyzer,I just can't open the result page.What I can see is just a message read "Please wait while the data is loading......". I try to submit the job again or just wait for hours and days,but still nothing changes.

Missing DB_GENECARDS_GENE_DISEASE_SCORE file?

When running the example from README.md:

perl disease_annotation.pl alzheimer -p -ph -logistic -out out/alzheimer_addon_all/out -addon DB_DISGENET_GENE_DISEASE_SCORE,DB_GAD_GENE_DISEASE_SCORE,DB_GENECARDS_GENE_DISEASE_SCORE -addon_weight 0.25

I get the error:

could not open ./lib/compiled_database/DB_GENECARDS_GENE_DISEASE_SCORE at disease_annotation.pl line 655.

Perhaps the script integrate_genecards_gene_disease.pl is used to generate DB_GENECARDS_GENE_DISEASE_SCORE but it requires the file raw_gene_cards, which according to the script should be in the lib directory but is also missing.

May you provide the DB_GENECARDS_GENE_DISEASE_SCORE file or let me know how I can generate it?

Thanks

program usage information cannot be printed out correctly

When running disease_annotation.pl without argument, the program usage information cannot be printed out correctly. Instead, a message Can't open phenolyzer/disease_annotation.pl: No such file or directory at phenolyzer/disease_annotation.pl line 48. is shown. This happens whenever the software is called in a directory other than the phenolyzer directory.

the -out argument does not work correctly

The -out argument only works if I run the program in the phenolyzer installation directory. Otherwise no output files will be generated and no warning/error messages are shown.

Visualize results like a website

Dear developer, hello

Why can't programs in the github repository draw visualizations like those on your website, or can you explain the detailed methods? These are not covered in your readme

Thank you for your answer

网址打不开？

最近网址一直打不开

Rcpp.so,slam.so,wordcloud.so for ARM

Hello team,
Can you provide the source code of the embedded .SO libs (Rcpp.so,slam.so,wordcloud.so),?Because I want run phenlolyzer on my ARM Server

Script used for precalculations?

Hello,

My apologies if I missed it in the repo, but could you point me to the script that was used to compute and zip the precalculated expansions and scores? I'm planning to use a tweaked version of the underlying databases and was hoping to re-pre-calculate the zip files.

Thank you very much,
Sam

Recommendations for maintaining external databases?

Hello,

I would like to use this tool but noticed the external databases have not been updated in a while. Are there any recommendations for maintaining these?