[Bioc-devel] FastqStreamer error in function context
On 05/09/2012 09:53 PM, Thomas Girke wrote:
When FastqStreamer or FastqSampler are called within another function in combination with a writeFastq step then this usually returns an error. However, the same code runs just fine outside of a function. Below is an example to reproduce this error.
Hi Thomas -- The example below fails because there are 256 records in the file, so for me the 52nd yield() returns length(fq) == 1 and the subset '2' is out of bounds. But maybe there is another example?
A small feature request for FastqStreamer would be an option to return the total number of reads stored in a fastq file as well as an option for accessing specific records by passing on an index vector.
For the first part, after the fact we have
> f
class: FastqStreamer
file: s_1_sequence.txt
status: n=5 current=1 added=256 total=256
with 'total=256' indicating that the streamer iterated over (i.e., the
file had) 256 records. This is actually accessible in the reference
class using the not-really-public (see the last lines of
example(FastqStreamer)) accessor
> f$status()
n current added total
5 1 256 256
which is a named integer vector. Is this what you were looking for?
I'll give the idea about selecting specific records some thought; I see
how it could be useful.
Martin
Best,
Thomas
Here is an example:
library(ShortRead)
sp<- SolexaPath(system.file('extdata', package='ShortRead'))
fl<- file.path(analysisPath(sp), "s_1_sequence.txt")
## Some function using FastqStreamer
test<- function(x=fl) {
f<- FastqStreamer(x, 5)
while (length(fq<- yield(f))) {
fqsub<- fq[1:2]
writeFastq(fqsub, "test.fastq", mode="a")
}
close(f)
}
test(x=fl)
Error in .IRanges.checkAndTranslateSingleBracketSubscript(x, i) :
subscript contains NAs or out of bounds indices
sessionInfo()
R version 2.15.0 alpha (2012-03-05 r58604)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.14.3 latticeExtra_0.6-19 RColorBrewer_1.0-5
[4] Rsamtools_1.8.4 lattice_0.20-6 Biostrings_2.24.1
[7] GenomicRanges_1.8.4 IRanges_1.14.2 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] Biobase_2.16.0 bitops_1.0-4.1 grid_2.15.0 hwriter_1.3 stats4_2.15.0
[6] tools_2.15.0 zlibbioc_1.2.0
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