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biocom-uib / vpf-tools

Virus Protein Family tools
BSD 3-Clause "New" or "Revised" License
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data-index.yaml #6

Closed gtsiamis closed 3 years ago

gtsiamis commented 3 years ago

I am trying to implement vpf-class to a set of assemblies that contain sequences from viruses. I have been able to install the app but I have a couple of questions with respect to the data-index.yaml file.

In this file the path of several reference files is provided. Is that correct? I have been able to download the reference files from the Supplementary files of the vpf-class manuscript? Is that OK or I need to download the files from another link?

The final_list.hmms file has been downloaded from the link provided.

Your assistance is greatly appreciated.

Regards George

michoug commented 3 years ago

Hi, Not a dev but here is my data-index.yaml

classificationFiles:
  baltimore:
    modelClassesFile: ./data/2019_VPF_BaltTax_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresBaltTax.tsv
  family:
    modelClassesFile: ./data/2019_VPF_FamTax_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresFamTax.tsv
  genus:
    modelClassesFile: ./data/2019_VPF_GenTax_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresGenTax.tsv
  host_domain:
    modelClassesFile: ./data/2019_VPF_DomHost_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresDomHost.tsv
  host_family:
    modelClassesFile: ./data/2019_VPF_FamHost_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresFamHost.tsv
  host_genus:
    modelClassesFile: ./data/2019_VPF_GenHost_REclassification_new.tsv
    scoreSamplesFile: ./data/2019_Uvigs_scoresGenHost.tsv

vpfsFile: ./data/final_list.hmms
gtsiamis commented 3 years ago

Hi,

And how I can download the tsv files?

regards George

michoug commented 3 years ago

Hi,

Here

http://bioinfo.uib.es/~recerca/VPF-Class/

Example : Summary and UViG Score samples http://bioinfo.uib.es/~recerca/VPF-Class/vpf_classification_summary/baltimore.tsv http://bioinfo.uib.es/~recerca/VPF-Class/uvigs_scores/2019_Uvigs_scoresBaltTax.tsv

bielr commented 3 years ago

Hi all,

Apologies for the delay, apparently notifications were disabled by default.

@michoug is correct, and the README is now fixed.

Thanks for the feedback!