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Question: Compareequence function is not running
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gravatar for susobhanbaidya
14 months ago by
susobhanbaidya0 wrote:

I have installed the  required packages properly. Now I crate two similar sequence by name X1.fa and X2.fa .

And try to run the following code. But getting uncanny error.

Please help me 

 

> library(CRISPRseek)
> outputDir <- getwd()
> inputFile1Path <- "X1.fa"
> inputFile2Path <- "X2.fa" 
> REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek")
> seqs <- compare2Sequences(inputFile1Path, inputFile2Path, outputDir = outputDir, 
+ REpatternFile = REpatternFile, overwrite = TRUE)
search for gRNAs for input file1...
Validating input ...
Searching for gRNAs ...
<simpleError in findgRNAs(inputFilePath, findPairedgRNAOnly = findPairedgRNAOnly,     annotatePaired = annotatePaired, pairOutputFile = pairOutputFile,     PAM = PAM, PAM.location = PAM.location, gRNA.pattern = gRNA.pattern,     PAM.size = PAM.size, gRNA.size = gRNA.size, min.gap = min.gap,     max.gap = max.gap, name.prefix = gRNA.name.prefix, format = format,     featureWeightMatrixFile = featureWeightMatrixFile, baseBeforegRNA = baseBeforegRNA,     baseAfterPAM = baseAfterPAM, calculategRNAEfficacy = TRUE,     efficacyFile = efficacyFile): inputfile specified as X1.fa does not exists!>
search for gRNAs for input file2...
Validating input ...
Searching for gRNAs ...
<simpleError in findgRNAs(inputFilePath, findPairedgRNAOnly = findPairedgRNAOnly,     annotatePaired = annotatePaired, pairOutputFile = pairOutputFile,     PAM = PAM, PAM.location = PAM.location, gRNA.pattern = gRNA.pattern,     PAM.size = PAM.size, gRNA.size = gRNA.size, min.gap = min.gap,     max.gap = max.gap, name.prefix = gRNA.name.prefix, format = format,     featureWeightMatrixFile = featureWeightMatrixFile, baseBeforegRNA = baseBeforegRNA,     baseAfterPAM = baseAfterPAM, calculategRNAEfficacy = TRUE,     efficacyFile = efficacyFile): inputfile specified as X2.fa does not exists!>
[1] "Scoring ..."
Error in .Call2("new_input_filexp", filepath, PACKAGE = "XVector") : 
  cannot open file 'X1.fa'

ADD COMMENTlink modified 14 months ago by daniel.vantwisk30 • written 14 months ago by susobhanbaidya0

This appears to be the exact same question as Not running the the code for compare2Sequences(.

ADD REPLYlink modified 14 months ago • written 14 months ago by daniel.vantwisk30
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