Entering edit mode
Marcus Davy
▴
390
@marcus-davy-5153
Last seen 6.1 years ago
Hi Martin,
when the FastqSampler uniformly samples from Fastq files, it appears
that
the header information in the id() accessor of a ShortReadQ object is
not
sorted in the sample with respect to tile information, as you would
expect
in the original source files.
I was wondering whether an argument (e.g. sortByID=TRUE/FALSE) would
be
worth implementing in FastqSampler to specify whether to sort the
sampled
reads by their IDs rather than sorting manually after taking a sample?
cheers,
Marcus
## Using ShortRead example
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")
## Load Fastq data to change id information
rfq <- readFastq(fl)
## No tile information in example
id(rfq)
## Make up some new headers in the form;
## @HWI-EAS88:187:C0101VACXX:2:2206:9399:51464 1:N:0:
tile <- rep(c(1001:(1001+7)), each=length(rfq)/8)
x <- gsub(".+_(\\d+)_\\d+$", "\\1", id(rfq))
y <- gsub(".+_\\d+_(\\d+)$", "\\1", id(rfq))
ids <- paste("@HWI-EAS88:187:C0101VACXX:2:", tile, ":", x, ":", y, "
1:N:0:", sep="")
## Hack overlaying ids with additional tile information
rfq@id <- BStringSet(ids)
## Write to a tmp file
writeFastq(rfq, "/tmp/example.fastq")
f <- open(FastqSampler("/tmp/example.fastq", 50))
## Sample
set.seed(42)
fqSample <- yield(f)
close(f)
## Tile information is randomly ordered
id(fqSample)
sapply(strsplit(as.character(id(fqSample)), ":"), function(x)x[5])
## Manually sorting the ids
o <- srorder(id(fqSample))
fqSorted <- fqSample[o]
id(fqSorted)
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.16.1 latticeExtra_0.6-24 RColorBrewer_1.0-5
[4] Rsamtools_1.10.1 lattice_0.20-10 Biostrings_2.26.2
[7] GenomicRanges_1.10.2 IRanges_1.16.2 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] Biobase_2.18.0 bitops_1.0-4.1 grid_2.15.0 hwriter_1.3
[5] parallel_2.15.0 stats4_2.15.0 tools_2.15.0 zlibbioc_1.4.0
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