search

daisybio / ASimulatoR

ASimulatoR: splice-aware RNA-seq data simulation https://doi.org/10.1093/bioinformatics/btab142
GNU Lesser General Public License v3.0
6 stars 1 forks source link

GFF3 File #7

Open igonzalsbmc opened 1 month ago

igonzalsbmc commented 1 month ago

What am I doing incorrectly? I'm receiving this error message when I use an annotation file in my own disk:

Code:

gtf_file <- system.file('extdata', '../genome/gencode.vM25.primary_assembly.annotation.gff3', package = 'ASimulatoR')
exon_superset <- get_exon_supersets(gtf_file)

Error:

(base) igonzals9cf2:code israelgonzalez$ Rscript asimulator.R 
Skipping install of 'ASimulatoR' from a github remote, the SHA1 (ad721cae) has not changed since last install.
  Use `force = TRUE` to force installation
importing gtf/gff...
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'con' in selecting a method for function 'import': Cannot detect format (no extension found in file name)
Calls: get_exon_supersets ... <Anonymous> -> <Anonymous> -> import -> FileForFormat
Execution halted
quirinmanz commented 1 month ago

Hi, Sorry for the late reply. Did everything work well with the installation of the package via remotes?