Question: Pulling Genbank Annotation Information via library(genbankr)
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gravatar for story.benjamin
7 months ago by
story.benjamin10 wrote:

I am trying to pull a specific GenBank entry off of the NCBI database using the genbankr library. My hope was to have all the feature information in a more "R friendly" (e.g. GRanges) format so I could incorporate it into my analysis. Other IDs seem to work but this one was giving me trouble.

This is the location of the entry on the web:

https://www.ncbi.nlm.nih.gov/nuccore/AJ000387.1

I tried both downloading the entry manually (.gb file - both 'full' and 'standard') and loading into the program by calling the following functions, respectively:

gb = readGenBank('./zam.gb')

and

gba = GBAccession("AJ000387.1")
gb = readGenBank(gba, partial=TRUE)

Apparently this format should be possible to import (and works for other GenBank entries) but I am running into some strange error:

Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘getListElement’ for signature ‘"GRanges"’

Is there any easy way to fix this and/or is this a type of entry the package cannot handle by nature?

Thanks for your time.

Ben

---

R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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

other attached packages:
[1] genbankr_1.8.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18                compiler_3.5.0
 [3] GenomeInfoDb_1.16.0         XVector_0.20.0
 [5] GenomicFeatures_1.32.0      prettyunits_1.0.2
 [7] bitops_1.0-6                tools_3.5.0
 [9] zlibbioc_1.26.0             progress_1.2.0
[11] biomaRt_2.36.1              digest_0.6.15
[13] bit_1.1-14                  jsonlite_1.5
[15] BSgenome_1.48.0             lattice_0.20-35
[17] RSQLite_2.1.1               memoise_1.1.0
[19] pkgconfig_2.0.1             rlang_0.2.1
[21] Matrix_1.2-14               DelayedArray_0.6.3
[23] DBI_1.0.0                   curl_3.2
[25] parallel_3.5.0              GenomeInfoDbData_1.1.0
[27] rtracklayer_1.40.3          stringr_1.3.1
[29] httr_1.3.1                  Biostrings_2.48.0
[31] S4Vectors_0.18.3            IRanges_2.14.10
[33] hms_0.4.2                   grid_3.5.0
[35] stats4_3.5.0                bit64_0.9-7
[37] Biobase_2.40.0              R6_2.2.2
[39] AnnotationDbi_1.42.1        rentrez_1.2.1
[41] BiocParallel_1.14.2         XML_3.98-1.11
[43] blob_1.1.1                  magrittr_1.5
[45] matrixStats_0.54.0          GenomicAlignments_1.16.0
[47] Rsamtools_1.32.2            BiocGenerics_0.26.0
[49] GenomicRanges_1.32.6        SummarizedExperiment_1.10.1
[51] assertthat_0.2.0            stringi_1.2.3
[53] RCurl_1.95-4.10             VariantAnnotation_1.26.1
[55] crayon_1.3.4

annotation genbankr genbank • 172 views
ADD COMMENTlink modified 7 months ago • written 7 months ago by story.benjamin10

So I think the problem has something to do with the command:

exns = stack(exns)

which is made by the make_exongr() function, made by make_gbrecord(), which is made by the original readGenBank() command

I hacked together a workaround for my purposes but I'm not sure if this is a bug or a 1-off scenario that someone might be interested in addressing.

Feel free to close.

 

 

ADD REPLYlink modified 7 months ago • written 7 months ago by story.benjamin10

Hi, 

I am having exactly the same problem with the Genbank id: AM749299.1. Did you find a solution for this/would you be happy to share your workaround?

Thanks!

ADD REPLYlink written 5 months ago by cristina.venturini.110
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