Question

customProDB: error aberrant fasta from indels

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kristenbeck527 • 0

@kristenbeck527-8349

Last seen 9.4 years ago

United States

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

Steps related to generating the aberrant fasta:

vcf = InputVcf(vcffile)
index <- which(values(vcf[[1]])[['INDEL']]==TRUE) # returns 1,333 indels
indelloc <- Varlocation(indelvcf,txdb,ids) # 1,333 indels found
postable_indel <- Positionincoding(indelvcf, exon) # 35 observations
txlist_indel <- unique(postable_indel[, 'txid']) # still 35 indels
codingseq_indel <- procodingseq[procodingseq[, 'tx_id'] %in% txlist_indel, ] # now only 30 indels
Outputaberrant(postable_indel, 
               coding=codingseq_indel,
               proteinseq=proteinseq, 
               outfile=outfile, ids=ids)

This returns the following error:

Error in translate(DNAStringSet(total[, "coding"])) : 
error in evaluating the argument 'x' in selecting a method for function 'translate': Error in width(x) : NAs in 'x' are not supported

Any help is appreciated as always.

indel customprodb fasta variantannotation • 2.1k views

ADD COMMENT • link updated 9.4 years ago by xiaojing.wang ▴ 50 • written 9.4 years ago by kristenbeck527 • 0

score 2 · Accepted Answer · 2015-07-09

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xiaojing.wang ▴ 50

@xiaojingwang-8081

Last seen 6.3 years ago

United States

Please send the VCF file to my email address and also paste the output of sessionInfo() of your R environment. Xiaojing From: kristenbeck527 [bioc] [mailto:noreply@bioconductor.org] Sent: Thursday, July 09, 2015 2:57 PM To: Wang, Xiaojing Subject: [bioc] customProDB: error aberrant fasta from indels Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User kristenbeck527<https: support.bioconductor.org="" u="" 8349=""/> wrote Question: customProDB: error aberrant fasta from indels<https: support.bioconductor.org="" p="" 69741=""/>: I am trying to make a variant called fasta file using CustomProDB. I am able to generate the SNV fasta but running into issues generating the indel derived fasta. Steps related to generating the aberrant fasta: vcf = InputVcf(vcffile) index <- which(values(vcf[[1]])[['INDEL']]==TRUE) # returns 1,333 indels indelloc <- Varlocation(indelvcf,txdb,ids) # 1,333 indels found postable_indel <- Positionincoding(indelvcf, exon) # 35 observations txlist_indel <- unique(postable_indel[, 'txid']) # still 35 indels codingseq_indel <- procodingseq[procodingseq[, 'tx_id'] %in% txlist_indel, ] # now only 30 indels Outputaberrant(postable_indel, coding=codingseq_indel, proteinseq=proteinseq, outfile=outfile, ids=ids) This returns the following error: Error in translate(DNAStringSet(total[, "coding"])) : error in evaluating the argument 'x' in selecting a method for function 'translate': Error in width(x) : NAs in 'x' are not supported Any help is appreciated as always. ________________________________ Post tags: indel, customprodb, fasta, variantannotation You may reply via email or visit customProDB: error aberrant fasta from indels

ADD COMMENT • link 9.4 years ago xiaojing.wang ▴ 50

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Here is my session info:

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] customProDB_1.6.0 biomaRt_2.22.0 AnnotationDbi_1.28.2
[4] GenomeInfoDb_1.2.5 Biobase_2.26.0 IRanges_2.0.1
[7] S4Vectors_0.4.0 BiocGenerics_0.12.1

loaded via a namespace (and not attached):
[1] base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9
[4] BiocParallel_1.0.3 Biostrings_2.34.1 bitops_1.0-6
[7] brew_1.0-6 BSgenome_1.34.1 checkmate_1.6.0
[10] codetools_0.2-11 DBI_0.3.1 digest_0.6.8
[13] fail_1.2 foreach_1.4.2 GenomicAlignments_1.2.2
[16] GenomicFeatures_1.18.7 GenomicRanges_1.18.4 iterators_1.0.7
[19] magrittr_1.5 plyr_1.8.3 Rcpp_0.11.6
[22] RCurl_1.95-4.7 Rsamtools_1.18.3 RSQLite_1.0.0
[25] rtracklayer_1.26.3 sendmailR_1.2-1 stringi_0.5-5
[28] stringr_1.0.0 tools_3.1.3 VariantAnnotation_1.12.9
[31] XML_3.98-1.3 XVector_0.6.0 zlibbioc_1.12.0

ADD REPLY • link 9.4 years ago kristenbeck527 • 0

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Please use customProDB_1.8.2. http://bioconductor.org/packages/release/bioc/html/customProDB.html Xiaojing From: kristenbeck527 [bioc] [mailto:noreply@bioconductor.org] Sent: Friday, July 10, 2015 2:39 PM To: Wang, Xiaojing Subject: [bioc] C: customProDB: error aberrant fasta from indels Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User kristenbeck527<https: support.bioconductor.org="" u="" 8349=""/> wrote Comment: customProDB: error aberrant fasta from indels<https: support.bioconductor.org="" p="" 69741="" #69786="">: Here is my session info: > sessionInfo() R version 3.1.3 (2015-03-09) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.4 (Yosemite) 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] customProDB_1.6.0 biomaRt_2.22.0 AnnotationDbi_1.28.2 [4] GenomeInfoDb_1.2.5 Biobase_2.26.0 IRanges_2.0.1 [7] S4Vectors_0.4.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9 [4] BiocParallel_1.0.3 Biostrings_2.34.1 bitops_1.0-6 [7] brew_1.0-6 BSgenome_1.34.1 checkmate_1.6.0 [10] codetools_0.2-11 DBI_0.3.1 digest_0.6.8 [13] fail_1.2 foreach_1.4.2 GenomicAlignments_1.2.2 [16] GenomicFeatures_1.18.7 GenomicRanges_1.18.4 iterators_1.0.7 [19] magrittr_1.5 plyr_1.8.3 Rcpp_0.11.6 [22] RCurl_1.95-4.7 Rsamtools_1.18.3 RSQLite_1.0.0 [25] rtracklayer_1.26.3 sendmailR_1.2-1 stringi_0.5-5 [28] stringr_1.0.0 tools_3.1.3 VariantAnnotation_1.12.9 [31] XML_3.98-1.3 XVector_0.6.0 zlibbioc_1.12.0 ________________________________ Post tags: indel, customprodb, fasta, variantannotation You may reply via email or visit C: customProDB: error aberrant fasta from indels