Entering edit mode
Hello everybody,
The library ShortRead includes two very useful functions: readFastq()
and readFasta()
While readFastq() can open FASTQ files as either plain text or gzipped
files, readFasta() can only open files in plain text.
For example:
# FASTQ: success
> readFastq("t01213R0QU.fq.gz")
class: ShortReadQ
length: 43608 reads; width: 178..486 cycles
# FASTA: failure
> readFasta("t01213R0QU.P.fa.gz")
Error in .normargInputFilepath(filepath) :
file "t01213R0QU.P.fa.gz" has unsupported type: gzfile
Is this the current status or it's time for me to update my BioC?
Can someone offer a work around that does not involve decompressing
the FASTA file to disc? I tried, yet unsuccessfully:
readFasta(gzfile("t01213R0QU.P.fa.gz","r"))
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function ?readFasta? for
signature ?"gzfile"?
Thank you,
Ivan
> sessionInfo()
R Under development (unstable) (2012-11-30 r61184)
Platform: x86_64-unknown-linux-gnu (64-bit)
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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] Rsamtools_1.11.16 Biostrings_2.27.11 GenomicRanges_1.11.29
[4] IRanges_1.17.32 BiocGenerics_0.5.6
loaded via a namespace (and not attached):
[1] bitops_1.0-5 stats4_2.16.0 tools_2.16.0 zlibbioc_1.5.0