Ramzi,
In case you have trouble or don't want to install R-devel + Bioc-devel,
here is code that should work with release and devel (my sessionInfo
at the end):
library(Biostrings)
bset <- read.BStringSet("path/to/your/file", format="fastq")
dnaletter_cols <- as.integer(
BString(paste(DNA_ALPHABET, collapse=""))) + 1L
ndnaletter_per_string <-
rowSums(alphabetFrequency(bset)[ , dnaletter_cols])
which(ndnaletter_per_string != width(bset))
Cheers,
H.
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.14.12 IRanges_1.4.11
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 tools_2.10.1
Hervé Pagès wrote:
Hi Ramzi,
One thing you can try is loading your fastq file with:
library(Biostrings)
bset <- read.BStringSet("path/to/your/file", format="fastq")
Note the use of read.BStringSet() instead of read.DNAStringSet().
Since BString/BStringSet objects are not limited to the DNA alphabet
(see ?DNA_ALPHABET), you should be able to load your file even if
it contains non-DNA letters (unless it has other problems of course).
Then you can do something like:
ndnaletter_per_string <-
vcountPDict(BStringSet(DNA_ALPHABET), bset, collapse=2)
which(ndnaletter_per_string != width(bset))
to extract the list of fastq records (as an integer vector) that
contain at least 1 non-DNA letter. (Note that the code above works
only with R-devel + BioC-devel.)
That way you'll be able to know if you have records like this and
where they are.
readFastq() won't load a fastq file with non-DNA letters in it.
Cheers,
H.
Ramzi TEMANNI wrote:
Hi,
I'm encountering the following error when trying to load fastq file:
Error in .local(dirPath, pattern, ...) :
_DNAencode(): key 73 not in lookup table
Key 73 in ascii table is "I" (capital i)
Anyone had encountered such error before ?
Thanks in advance for your help
Regards,
Ramzi
sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.2.0 ShortRead_1.4.0 lattice_0.18-3
BSgenome_1.14.2
[5] Biostrings_2.14.12 IRanges_1.4.11
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.1 hwriter_1.1 RCurl_1.3-1 XML_2.6-0
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
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