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geno2proteo #49

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jeroen opened this issue Aug 14, 2019 · 1 comment

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@jeroen
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commented Aug 14, 2019

All test and examples fail in scan(). Maybe a perl issue?

library(geno2proteo)
# Registered S3 method overwritten by 'R.oo':
#  method        from       
#  throw.default R.methodsS3
example(generatingCDSaaFile)
# 
# gnCDSF>     # the data folder in this package
# gnCDSF>     dataFolder = system.file("extdata", package="geno2proteo") 
# 
# gnCDSF>     geneticCodeFile_line = file.path(dataFolder, 
# gnCDSF+                                     "geneticCode_standardTable_lines.txt")
# 
# gnCDSF>     gtfFile = file.path(dataFolder, 
# gnCDSF+                 "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
# 
# gnCDSF>     DNAfastaFile =  file.path(dataFolder, 
# gnCDSF+             "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
# 
# gnCDSF>     outputFolder = tempdir(); # using the current folder as output folder
# 
# gnCDSF>     # calling the function.
# gnCDSF>     generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
# gnCDSF+         gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
# Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
#   line 2 did not have 7 elements

@yaoyong02

@jeroen

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commented Aug 16, 2019

I think the error appears after running DNAseqTranslation_CDS.perl. The msys2 version of perl somehow inserts a \r into the data which R on Windows interprets as a linebreak in read.table()

rawToChar(readBin(filenameAllCDSdnaSeqAA, raw(),n = 100))
[1] "16\t2867270\t2867333\t+\tENST00000005995\t1\t0\r\tATGGGCGCGCGCGGGGCGCTGCTGCTGGCGCTGCTGCTGGCTCGGGCTGGACTCAGGA"
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