Search
Question: Compareequence function is not running
0
gravatar for susobhanbaidya
3 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 3 months ago by daniel.vantwisk30 • written 3 months ago by susobhanbaidya0

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

ADD REPLYlink modified 3 months ago • written 3 months ago by daniel.vantwisk30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 137 users visited in the last hour