problem using UniprotR's " GetFamily_Domains() "
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Entering edit mode
24 months ago
j.lunger18 ▴ 30

I'm having trouble using the GetFamily_Domains() function in Uniprot R. Here is my code after installing the package and adding it to my library:

uniprot_ID <- "Q9HCE5"
domain_list <- GetFamily_Domains(uniprot_ID)

"Warning message:In file(file, "rt") : cannot open URL 'http://www.uniprot.org/uniprot/?query=accession:Q9HCE5&format=tab&columns=comment(DOMAIN),comment(SIMILARITY),families,feature(COILED COIL),feature(COMPOSITIONAL BIAS),feature(DOMAIN EXTENT),feature(MOTIF),feature(REGION),feature(REPEAT),feature(ZINC FINGER)': HTTP status was '400 Bad Request'"

When I copy the URL and paste it into chrome it opens fine... so I'm not sure what to do here.

r uniprot protein domains functional domains • 642 views
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Entering edit mode

Your URL seems correct in principle, and the http request is redirected to https. But it might help to use https instead of http straightaway? I'm not familiar with this R package. https://www.uniprot.org/uniprot/?query=accession:Q9HCE5&format=tab&columns=comment(DOMAIN),comment(SIMILARITY),families,feature(COILED%20COIL),feature(COMPOSITIONAL%20BIAS),feature(DOMAIN%20EXTENT),feature(MOTIF),feature(REGION),feature(REPEAT),feature(ZINC%20FINGER)

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