I a trying hard to make a proper txdb object that I can ultimately use with gDNAx package. I raised a separate issue here but I have realized that it's not gDNAx's problem but is actually about how the txdb object is created. I have downloaded the FASTA file and GTF file from ToxoDB from here and I have been trying hard to make a proper txdb object on which when I run seqlevelsStyle and genomeStyles should not throw an error. But it has proved to be a difficult task. I am not sure anymore what's the right way to do this so I am choosing to ask it here.

## Read files
gtf_file <- "ToxoDB-67_TgondiiME49.gtf"
fasta_file <- "ToxoDB-67_TgondiiME49_Genome.fasta"

## Making a txdb object
gff <- makeTxDbFromGFF(gtf_file,format = "gtf",organism = "Toxoplasma gondii",taxonomyId=508771, dataSource = "ToxoDB release 67")


## Maybe the chromosome information should be added
library(GenomicFeatures)
library(Biostrings)
library(Rsamtools)

fa <- FaFile(fasta_file)
fa_seqinfo <- seqinfo(fa)
seqinfo(gff) <- seqinfo(fa) ## Doesn't work
pruned_fa_seqinfo <- keepSeqlevels(fa_seqinfo, seqlevels(gff)) ## because the order of chromosome in GFF and FASTA file doesn't match. So to match that.
#seqinfo(gff) <- pruned_fa_seqinfo ## Doesn't work so let's rerun the makeTxDbFromGFF with this object pruned_fa_seqinfo
identical(seqlevels(gff), seqlevels(pruned_fa_seqinfo))  

## now using to recreate toxodb object with chromosome information
gff <- makeTxDbFromGFF(gtf_file,format = "gtf",organism = "Toxoplasma gondii",taxonomyId=508771, dataSource = "ToxoDB release 67",chrominfo = pruned_fa_seqinfo)

seqlevelsStyle(gff)
Error in seqlevelsStyle(seqlevels) : 
  The style does not have a compatible entry for the species supported by Seqname. Please see
  genomeStyles() for supported species/style

genomeStyles(gff)
Error in strsplit(organism, "_| ") : non-character argument

seqlevelsStyle(gff) <- "NCBI"
Error in .replace_seqlevels_style(x_seqlevels, value) : 
  found no sequence renaming map compatible with seqname style "NCBI" for this object

seqinfo(gff)
Seqinfo object with 436 sequences from an unspecified genome:
  seqnames       seqlengths isCircular genome
  KE138841            35372       <NA>   <NA>
  KE138851            13341       <NA>   <NA>
  KE138856             1030       <NA>   <NA>
  KE138857             1121       <NA>   <NA>
  KE138861             3123       <NA>   <NA>
  ...                   ...        ...    ...
  TGME49_chrVIIa    4541629       <NA>   <NA>
  TGME49_chrVIIb    5069724       <NA>   <NA>
  TGME49_chrX       7486190       <NA>   <NA>
  TGME49_chrXI      6623461       <NA>   <NA>
  TGME49_chrXII     7094428       <NA>   <NA>

Is this for genome assembly TGA4? https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006565.2/

If that's the case then:

library(txdbmaker)
gtf <- "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/565/GCF_000006565.2_TGA4/GCF_000006565.2_TGA4_genomic.gtf.gz"
txdb <- makeTxDbFromGFF(gtf, organism="Toxoplasma gondii ME49", taxonomyId=508771)
genome(txdb) <- "TGA4"

seqinfo(txdb)
# Seqinfo object with 437 sequences from TGA4 genome; no seqlengths:
#   seqnames       seqlengths isCircular genome
#   NC_001799.1          <NA>       <NA>   TGA4
#   NC_031467.1          <NA>       <NA>   TGA4
#   NC_031468.1          <NA>       <NA>   TGA4
#   NC_031469.1          <NA>       <NA>   TGA4
#   NC_031470.1          <NA>       <NA>   TGA4
#   ...                   ...        ...    ...
#   NW_017383901.1       <NA>       <NA>   TGA4
#   NW_017383916.1       <NA>       <NA>   TGA4
#   NW_017383917.1       <NA>       <NA>   TGA4
#   NW_017383919.1       <NA>       <NA>   TGA4
#   NW_017383924.1       <NA>       <NA>   TGA4

The sequence names here are the RefSeq accessions. For some reason switching to the NCBI names doesn't work for this assembly (I would need to investigate why). But we can always do this renaming ourselves "by hand":

chrominfo <- getChromInfoFromNCBI("TGA4")

chrominfo[1:9 , c("RefSeqAccn", "SequenceName")]
#    RefSeqAccn   SequenceName
# 1 NC_031467.1   TGME49_chrIa
# 2 NC_031468.1   TGME49_chrIb
# 3 NC_031469.1   TGME49_chrII
# 4 NC_031470.1  TGME49_chrIII
# 5 NC_031471.1   TGME49_chrIV
# 6 NC_031472.1    TGME49_chrV
# 7 NC_031473.1   TGME49_chrVI
# 8 NC_031474.1 TGME49_chrVIIa
# 9 NC_031475.1 TGME49_chrVIIb

m <- match(seqlevels(txdb), chrominfo$RefSeqAccn)

seqlevels(txdb) <- chrominfo[m , "SequenceName"]

seqinfo(txdb)
# Seqinfo object with 437 sequences from TGA4 genome; no seqlengths:
#   seqnames      seqlengths isCircular genome
#   Pltd                <NA>       <NA>   TGA4
#   TGME49_chrIa        <NA>       <NA>   TGA4
#   TGME49_chrIb        <NA>       <NA>   TGA4
#   TGME49_chrII        <NA>       <NA>   TGA4
#   TGME49_chrIII       <NA>       <NA>   TGA4
#   ...                  ...        ...    ...
#   asmbl.1867          <NA>       <NA>   TGA4
#   asmbl.1884          <NA>       <NA>   TGA4
#   asmbl.1885          <NA>       <NA>   TGA4
#   asmbl.1889          <NA>       <NA>   TGA4
#   asmbl.1912          <NA>       <NA>   TGA4

seqlevelsStyle(txdb)
# [1] "NCBI"

Note that the chrominfo data.frame obtained with getChromInfoFromNCBI() contains a lot of information about the sequences including their lengths. Unfortunately you cannot add/modify the seqlengths of a TxDb object after it has been created. If you really want them in your TxDb object you need to pass that information at creation-time thru the chrominfo argument of the makeTxDbFromGFF() function.

Hope this helps,

H.

Your post title is misleading. You have no problem whatsoever generating the TxDb, the problem is using it with gDNAx, which attempts to subset to the standard chromosomes, which requires knowing the genome style, and there are only a handful of species for which that is possible:

> names(genomeStyles())
 [1] "Arabidopsis_thaliana"    
 [2] "Caenorhabditis_elegans"  
 [3] "Canis_familiaris"        
 [4] "Cyanidioschyzon_merolae" 
 [5] "Drosophila_melanogaster" 
 [6] "Gossypium_hirsutum"      
 [7] "Homo_sapiens"            
 [8] "Mus_musculus"            
 [9] "Oryza_sativa"            
[10] "Populus_trichocarpa"     
[11] "Rattus_norvegicus"       
[12] "Saccharomyces_cerevisiae"
[13] "Zea_mays"

Any species not on that list will not be amenable to subsetting to standard chromosomes or changing the genome style. There may be a simple workaround, and if so I imagine either Robert Castelo or Herve Pages will be along soon enough to point it out. But I personally have never found a way to specify the standard chromosomes or genome style directly.