Having trouble with the GFF3. Could you provide a reprex (see the FAQ) using the example fasta file and an appropriate GFF3?
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# BiocManager::install("Biostrings")
library(ape)
library(Biostrings)
#> Loading required package: BiocGenerics
#>
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#>
#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
#> table, tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> Warning: package 'S4Vectors' was built under R version 4.3.1
#> Loading required package: stats4
#>
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#>
#> findMatches
#> The following objects are masked from 'package:base':
#>
#> expand.grid, I, unname
#> Loading required package: IRanges
#> Warning: package 'IRanges' was built under R version 4.3.1
#> Loading required package: XVector
#> Loading required package: GenomeInfoDb
#> Warning: package 'GenomeInfoDb' was built under R version 4.3.1
#>
#> Attaching package: 'Biostrings'
#> The following object is masked from 'package:ape':
#>
#> complement
#> The following object is masked from 'package:base':
#>
#> strsplit
## Read a non-compressed FASTA files:
filepath1 <- system.file("extdata", "someORF.fa", package="Biostrings")
fasta.seqlengths(filepath1, seqtype="DNA")
#> YAL001C TFC3 SGDID:S0000001, Chr I from 152168-146596, reverse complement, Verified ORF
#> 5573
#> YAL002W VPS8 SGDID:S0000002, Chr I from 142709-148533, Verified ORF
#>
g <- read.gff("/Users/ro/projects/demo/examp.gff3", na.strings = c(".", "?"), GFF3 = TRUE)
#> Error in scan(file, w, sep = "\t", quote = "", quiet = TRUE, na.strings = na.strings, :
scan() expected 'an integer', got '|ST4.03ch01|.|PCR_product|5319288|5319529|.|+|.|Name=ARM01-007;Note=validatedmarker|'