Error in parseGenBank
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Entering edit mode
@ashleydederich-21214
Last seen 2.2 years ago

Hi all,

I am trying to parse through a GenBank file and I keep getting this weird error :

parseGenBank(file)

Error in .Call2("new_XString_from_CHARACTER", class(x0), string, start,  : 
  key 79 (char 'O') not in lookup table

traceback()
9: .Call2("new_XString_from_CHARACTER", class(x0), string, start, 
       width, lkup, PACKAGE = "Biostrings")
8: make_XString_from_string(x0, string, start(solved_SEW), width(solved_SEW))
7: make_XString_from_string(x0, string, start(solved_SEW), width(solved_SEW))
6: .charToXString(seqtype, x, start, end, width)
5: XString("DNA", x, start = start, width = nchar)
4: XString("DNA", x, start = start, width = nchar)
3: DNAString(chars)
2: readOrigin(spl[["ORIGIN"]], seqtype = seqtype)
1: parseGenBank(files, ret.anno = FALSE)

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] genbankr_1.12.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1                  BiocManager_1.30.4         
 [3] compiler_3.6.0              GenomeInfoDb_1.20.0        
 [5] XVector_0.24.0              GenomicFeatures_1.36.3     
 [7] prettyunits_1.0.2           bitops_1.0-6               
 [9] tools_3.6.0                 zlibbioc_1.30.0            
[11] progress_1.2.2              biomaRt_2.40.1             
[13] digest_0.6.19               bit_1.1-14                 
[15] BSgenome_1.52.0             lattice_0.20-38            
[17] RSQLite_2.1.1               memoise_1.1.0              
[19] pkgconfig_2.0.2             rlang_0.4.0                
[21] Matrix_1.2-17               DelayedArray_0.10.0        
[23] DBI_1.0.0                   parallel_3.6.0             
[25] GenomeInfoDbData_1.2.1      rtracklayer_1.44.0         
[27] stringr_1.4.0               httr_1.4.0                 
[29] Biostrings_2.52.0           S4Vectors_0.22.0           
[31] IRanges_2.18.1              hms_0.4.2                  
[33] grid_3.6.0                  stats4_3.6.0               
[35] bit64_0.9-7                 Biobase_2.44.0             
[37] R6_2.4.0                    AnnotationDbi_1.46.0       
[39] tcltk_3.6.0                 BiocParallel_1.18.0        
[41] XML_3.98-1.20               blob_1.1.1                 
[43] magrittr_1.5                matrixStats_0.54.0         
[45] GenomicAlignments_1.20.1    Rsamtools_2.0.0            
[47] BiocGenerics_0.30.0         GenomicRanges_1.36.0       
[49] SummarizedExperiment_1.14.0 assertthat_0.2.1           
[51] stringi_1.4.3               RCurl_1.95-4.12            
[53] VariantAnnotation_1.30.1    crayon_1.3.4 

It seems to me like it is not recognizing the letter "O". Unsure how to fix this.

Thank you, Ashley

genbankr parseGenBank gbk error • 294 views
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