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bdaisley / isolateR

Automated processing of Sanger sequencing data, taxonomic profiling, and generation of microbial strain libraries
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Error with isoTAX db specification #5

Closed vancurens closed 5 months ago

vancurens commented 6 months ago

IsolateR version 0.0.0.9003

The database variable in isoTax should be able to accept the argument "16S|ITS" for the use of multiple databases in vsearch but results in an error. Also noted that setting to ITS will just result in the 16S database being installed.

> isoTAX.S4 <- isoTAX(input=in2,
+                     export_html=TRUE,
+                     export_csv=TRUE,
+                     db="16S|ITS",
+                     quick_search=FALSE)

Detecting operating system...

Operating system is ---> Windows-based <---
VSEARCH already downloaded

Staging files
Error in utils::download.file(eval(parse(text = paste(dblink.list)[names(dblink.list) %in%  : 
  invalid 'url' argument
> isoTAX.S4 <- isoTAX(input=in2,
+                     export_html=TRUE,
+                     export_csv=TRUE,
+                     db="16S,ITS",
+                     quick_search=FALSE)

Detecting operating system...

Operating system is ---> Windows-based <---
VSEARCH already downloaded

Staging files
Error in utils::download.file(eval(parse(text = paste(dblink.list)[names(dblink.list) %in%  : 
  invalid 'url' argument
> isoTAX.S4 <- isoTAX(input=in2,
+                     export_html=TRUE,
+                     export_csv=TRUE,
+                     db="ITS",
+                     quick_search=FALSE)

Detecting operating system...

Operating system is ---> Windows-based <---
VSEARCH already downloaded

Staging files
trying URL 'https://ftp.ncbi.nlm.nih.gov/refseq/TargetedLoci/Bacteria/bacteria.16SrRNA.fna.gz'
Content type 'application/x-gzip' length 7820305 bytes (7.5 MB)
downloaded 7.5 MB
vancurens commented 5 months ago

Solved in commits d2963fe and d86d77c.