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Question: customProDB: error aberrant fasta from indels
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gravatar for kristenbeck527
3.6 years ago by
United States
kristenbeck5270 wrote:

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.

ADD COMMENTlink modified 3.6 years ago by xiaojing.wang50 • written 3.6 years ago by kristenbeck5270
Answer: customProDB: error aberrant fasta from indels
2
gravatar for xiaojing.wang
3.6 years ago by
United States
xiaojing.wang50 wrote:
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 COMMENTlink written 3.6 years ago by xiaojing.wang50

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 REPLYlink written 3.6 years ago by kristenbeck5270
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
ADD REPLYlink written 3.6 years ago by xiaojing.wang50

Excellent! It worked. Thank you.

 

ADD REPLYlink written 3.6 years ago by kristenbeck5270
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