Hello.

I used Augustus to provide an annotation in gff3 format for my species, which does not have a published genome, against zebrafish. I am able to load my gff with makeTxDbFromGFF, however assignChromosomeRegion gives me an error regarding seqlevelsStyle.

Some lines from my gff:

LG1 AUGUSTUS gene 139 1546 0.57 + . ID=g1

LG1 AUGUSTUS transcript 139 735 0.32 + . ID=g1.t1;Parent=g1

LG1 AUGUSTUS start_codon 139 141 . + 0 Parent=g1.t1

LG1 AUGUSTUS intron 365 460 1 + . Parent=g1.t1

LG1 AUGUSTUS CDS 139 364 0.81 + 0 ID=g1.t1.cds;Parent=g1.t1

LG1 AUGUSTUS CDS 461 735 0.36 + 2 ID=g1.t1.cds;Parent=g1.t1

LG1 AUGUSTUS stop_codon 733 735 . + 0 Parent=g1.t1

My code and session info are found below.

Help appreciated. Thank you.

>GSnap_txDB <- makeTxDbFromGFF("completeallon", format=c("gff3"))
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type stop_codon.
  This information was ignored.
> PopSt_nonsig_achr <-assignChromosomeRegion(popSt_nonsig, nucleotideLevel=FALSE, 
+                                            precedence=c("Exons", "Introns"), 
+                                            TxDb=GSnap_txDB)
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



```r
sessionInfo( )
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rtracklayer_1.58.0     limma_3.54.2           mygene_1.34.0          ChIPpeakAnno_3.32.0   
 [5] genomation_1.30.0      GenomicFeatures_1.50.4 AnnotationDbi_1.60.2   Biobase_2.58.0        
 [9] ggplot2_3.4.2          pheatmap_1.0.12        reshape2_1.4.4         RColorBrewer_1.1-3    
[13] VennDiagram_1.7.3      futile.logger_1.4.3    methylKit_1.27.1       GenomicRanges_1.50.2  
[17] GenomeInfoDb_1.34.9    IRanges_2.32.0         S4Vectors_0.36.2       BiocGenerics_0.44.0   
[21] vcfR_1.14.0           

loaded via a namespace (and not attached):
  [1] backports_1.4.1             Hmisc_5.1-0                 BiocFileCache_2.6.1        
  [4] plyr_1.8.8                  lazyeval_0.2.2              splines_4.2.2              
  [7] BiocParallel_1.32.6         gridBase_0.4-7              digest_0.6.31              
 [10] htmltools_0.5.5             ensembldb_2.22.0            fansi_1.0.4                
 [13] checkmate_2.2.0             magrittr_2.0.3              memoise_2.0.1              
 [16] BSgenome_1.66.3             cluster_2.1.4               tzdb_0.4.0                 
 [19] InteractionSet_1.26.1       Biostrings_2.66.0           readr_2.1.4                
 [22] matrixStats_1.0.0           R.utils_2.12.2              bdsmatrix_1.3-6            
 [25] prettyunits_1.1.1           colorspace_2.1-0            blob_1.2.4                 
 [28] rappdirs_0.3.3              xfun_0.39                   dplyr_1.1.2                
 [31] jsonlite_1.8.7              crayon_1.5.2                RCurl_1.98-1.12            
 [34] graph_1.76.0                impute_1.72.3               survival_3.4-0             
 [37] ape_5.7-1                   glue_1.6.2                  gtable_0.3.3               
 [40] zlibbioc_1.44.0             XVector_0.38.0              DelayedArray_0.24.0        
 [43] scales_1.2.1                futile.options_1.0.1        mvtnorm_1.2-2              
 [46] DBI_1.1.3                   Rcpp_1.0.10                 plotrix_3.8-2              
 [49] htmlTable_2.4.1             viridisLite_0.4.2           progress_1.2.2             
 [52] emdbook_1.3.13              foreign_0.8-83              bit_4.0.5                  
 [55] mclust_6.0.0                sqldf_0.4-11                Formula_1.2-5              
 [58] htmlwidgets_1.6.2           httr_1.4.6                  pkgconfig_2.0.3            
 [61] XML_3.99-0.14               R.methodsS3_1.8.2           nnet_7.3-18                
 [64] dbplyr_2.3.3                utf8_1.2.3                  tidyselect_1.2.0           
 [67] rlang_1.1.0                 munsell_0.5.0               tools_4.2.2                
 [70] cachem_1.0.8                cli_3.6.0                   gsubfn_0.7                 
 [73] generics_0.1.3              RSQLite_2.3.1               fastseg_1.44.0             
 [76] evaluate_0.21               stringr_1.5.0               fastmap_1.1.1              
 [79] yaml_2.3.7                  knitr_1.43                  bit64_4.0.5                
 [82] KEGGREST_1.38.0             AnnotationFilter_1.22.0     RBGL_1.74.0                
 [85] nlme_3.1-160                formatR_1.14                R.oo_1.25.0                
 [88] xml2_1.3.4                  biomaRt_2.54.1              compiler_4.2.2             
 [91] rstudioapi_0.15.0           filelock_1.0.2              curl_5.0.1                 
 [94] png_0.1-8                   tibble_3.2.1                stringi_1.7.12             
 [97] lattice_0.20-45             ProtGenerics_1.30.0         Matrix_1.5-1               
[100] vegan_2.6-4                 permute_0.9-7               multtest_2.54.0            
[103] vctrs_0.6.3                 pillar_1.9.0                lifecycle_1.0.3            
[106] BiocManager_1.30.21.1       data.table_1.14.8           bitops_1.0-7               
[109] qvalue_2.30.0               R6_2.5.1                    BiocIO_1.8.0               
[112] gridExtra_2.3               KernSmooth_2.23-20          codetools_0.2-18           
[115] lambda.r_1.2.4              MASS_7.3-58.1               gtools_3.9.4               
[118] chron_2.3-61                proto_1.0.0                 SummarizedExperiment_1.28.0
[121] rjson_0.2.21                withr_2.5.0                 pinfsc50_1.2.0             
[124] regioneR_1.30.0             GenomicAlignments_1.34.1    Rsamtools_2.14.0           
[127] GenomeInfoDbData_1.2.9      mgcv_1.8-41                 parallel_4.2.2             
[130] hms_1.1.3                   rpart_4.1.19                coda_0.19-4                
[133] rmarkdown_2.23              MatrixGenerics_1.10.0       bbmle_1.0.25               
[136] seqPattern_1.30.0           base64enc_0.1-3             numDeriv_2016.8-1.1        
[139] restfulr_0.0.15

That error comes from GenomeInfoDb and is what you get when you try to change the seqlevelsStyle on a TxDb that isn't common. As the error says, you can run genomeStyles() to see the species that will work (yours isn't in that list).

An alternative is to ensure that the seqlevels in your input GRanges match up with the seqlevels in your TxDb, and if so, you can use the legacy method for assignChromosomeRegion, where you supply the exons, TSS, utr5 and utr3 GRanges directly instead of having the function do that for you. You will get a warning, but it should work.

Arguments:

peaks.RD: peaks in GRanges: See example below

    exon: exon data obtained from getAnnotation or customized
          annotation of class GRanges containing additional variable:
          strand (1 or + for plus strand and -1 or - for minus strand).
          This parameter is for backward compatibility only.  'TxDb'
          should be used instead.

     TSS: TSS data obtained from getAnnotation or customized annotation
          of class GRanges containing additional variable: strand (1 or
          + for plus strand and -1 or - for minus strand). For example,
          data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37),
          data(TSS.rat.RGSC3.4) and data(TSS.zebrafish.Zv8). This
          parameter is for backward compatibility only. 'TxDb' should
          be used instead.

    utr5: 5 prime UTR data obtained from getAnnotation or customized
          annotation of class GRanges containing additional variable:
          strand (1 or + for plus strand and -1 or - for minus strand).
          This parameter is for backward compatibility only.  'TxDb'
          should be used instead.

    utr3: 3 prime UTR data obtained from getAnnotation or customized
          annotation of class GRanges containing additional variable:
          strand (1 or + for plus strand and -1 or - for minus strand).
          This parameter is for backward compatibility only.  'TxDb'
          should be used instead.