[Bioc-devel] Append/combine option for filterFastq and similar?
On 04/21/2015 02:18 PM, Ryan C. Thompson wrote:
Hello,
Often when sequence data is delivered to me, I receive each sample in several
input files. Generally I want to get them into a single file ASAP, and the
filterFastq step would be a convenient place to do it. Is there any possibility
to add some way to append to an output file, or maybe automatically combine the
outputs of any files with the same destination file. For example:
filterFastq(files=c("input1.fastq", "input2.fastq"),
destinations="output.fastq", ...)
actually I think the implementation almost does as you want, though
'destination' needs to be replicated to be as long as the inputs
> tmp = tempfile()
> filterFastq(c(fl, fl), c(tmp, tmp), filter=fun)
[1] "/tmp/RtmpxGSJ7G/file265712b558a0" "/tmp/RtmpxGSJ7G/file265712b558a0"
attr(,"filter")
Reads KeptReads Nucl KeptNucl
s_1_sequence.txt 256 255 9216 9180
s_1_sequence.txt.1 256 255 9216 9180
> length(readLines(tmp)) / 4
[1] 510
I'll make this a little more convenient (no need to replicate 'destination') and
document the behavior.
Martin
could process both input files and write their combined output to the one specified output file. Normal recycling rules would apply for the "destinations" argument, and input files would be grouped by destination file and each processed sequentially into that destination file. (This design is kind of magic, but it avoids the annoying pattern of having to process files one-by-one in a loop with append=FALSE for the first file and append=TRUE for the rest. (Also appending to a compressed fastq might not work?) -Ryan
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793