customProDB: error aberrant fasta from SNV
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Last seen 5 weeks ago

I am trying to make a variant called fasta file using CustomProDB. I am able to generate the INDEL fasta but running into issues generating the SNV derived fasta.

Steps related to generating the aberrant fasta:

vcf <- InputVcf(vcffile)
index <- which(values(vcf[[1]])[['INDEL']]==TRUE)
indelvcf <- vcf[[1]][index] 

postable_snv <- Positionincoding(SNVvcf, exon)
postable_snv  # 41,803 observations

txlist <- unique(postable_snv[, 'txid']) 

codingseq <- procodingseq[procodingseq[, 'tx_id'] %in% txlist,]

mtab <- aaVariation(postable_snv, codingseq)

This returns the following error:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'unique': error in evaluating the argument 'x' in selecting a method for function 'substr': error in evaluating the argument 'x' in selecting a method for function 'translate': input must be a single non-NA string
In addition: Warning message:
In .Call2("DNAStringSet_translate", x, skip_code, dna_codes[codon_alphabet],  :
  last 2 bases were ignored

Here is my session info:

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BiocManager_1.30.17    GenomicFeatures_1.46.5 GenomicRanges_1.46.1   GenomeInfoDb_1.30.1    customProDB_1.34.0     AnnotationDbi_1.56.2   Biobase_2.54.0        
 [8] IRanges_2.28.0         S4Vectors_0.32.4       BiocGenerics_0.40.0    biomaRt_2.50.3        

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.6.0        httr_1.4.4                  bit64_4.0.5                 assertthat_0.2.1            BiocFileCache_2.2.1         blob_1.2.3                 
 [7] BSgenome_1.62.0             GenomeInfoDbData_1.2.7      Rsamtools_2.10.0            yaml_2.3.5                  progress_1.2.2              pillar_1.8.1               
[13] RSQLite_2.2.14              lattice_0.20-45             glue_1.6.2                  digest_0.6.29               XVector_0.34.0              plyr_1.8.7                 
[19] htmltools_0.5.3             Matrix_1.4-0                XML_3.99-0.10               pkgconfig_2.0.3             bookdown_0.31               zlibbioc_1.40.0            
[25] purrr_0.3.4                 BiocParallel_1.28.3         tibble_3.1.8                KEGGREST_1.34.0             generics_0.1.3              AhoCorasickTrie_0.1.2      
[31] ellipsis_0.3.2              cachem_1.0.6                SummarizedExperiment_1.24.0 cli_3.4.1                   magrittr_2.0.3              crayon_1.5.1               
[37] memoise_2.0.1               evaluate_0.16               fansi_1.0.3                 xml2_1.3.3                  tools_4.1.3                 prettyunits_1.1.1          
[43] hms_1.1.2                   BiocIO_1.4.0                lifecycle_1.0.1             matrixStats_0.62.0          stringr_1.4.1               DelayedArray_0.20.0        
[49] Biostrings_2.62.0           compiler_4.1.3              rlang_1.0.4                 grid_4.1.3                  RCurl_1.98-1.7              rstudioapi_0.14            
[55] VariantAnnotation_1.40.0    rjson_0.2.21                rappdirs_0.3.3              bitops_1.0-7                rmarkdown_2.16              restfulr_0.0.15            
[61] DBI_1.1.3                   curl_4.3.2                  R6_2.5.1                    GenomicAlignments_1.30.0    knitr_1.40                  dplyr_1.0.9                
[67] rtracklayer_1.54.0          fastmap_1.1.0               bit_4.0.4                   utf8_1.2.2                  filelock_1.0.2              stringi_1.7.8              
[73] parallel_4.1.3              Rcpp_1.0.9                  vctrs_0.4.1                 png_0.1-7                   dbplyr_2.2.1                tidyselect_1.1.2           
[79] xfun_0.32

Any help is appreciated as always.

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