[Bioc-devel] Reading FASTQ/BAM from open file handle?

Perfect, that's just what I wanted for Fastq files. Is there no R facility for
reading unindexed bam?
Well, playing around a little I did this in one terminal

~$ mkfifo myfifo
~$ cat tmp/bam/ex1.bam > myfifo

And then in R

   library(Rsamtools)
   scanBam("~/myfifo")  # or, e.g., readBamGappedAlignments("~/myfifo")

so I guess there are hacks. The way to iterate through a bam file is with BamFile

   bf = BamFile("myfifo", yieldSize=100000L)

but it's requiring an index when opened

 > open(bf)
Error in open.BamFile(bf) : failed to load BAM index
   file: myfifo
In addition: Warning message:
In open.BamFile(bf) : [bam_index_load] fail to load BAM index.

so you'd be stuck parsing the whole file...

Martin
On Tue 04 Dec 2012 02:47:56 PM PST, Martin Morgan wrote:
On 12/04/2012 01:27 PM, Ryan C. Thompson wrote:
Hi all,

I'm currently experimenting with using quip
(https://github.com/dcjones/quip#readme) to save disk space when
storing FASTQ
and BAM files. One thing that would be nice is to read
quip-compressed FASTQ or
BAM files directly into R. Obviously direct support for reading quip
compression
would be ideal, but in the short term, quip supports decompression to
standard
output, so if I could have R read FASTQ or BAM data from an open file
handle, I
could pipe the decompressed output to R's FASTQ or BAM reader
functions. Does
anyone know if this is possible?
ShortRead::FastqStreamer works with R connections, so for instance
after example(FastqStreamer)

  cmd = sprintf("cat %s", fl)
  p = pipe(cmd)
  strm = FastqStreamer(p, 50)
  yield(strm)
  yield(strm)

Rsamtools::scanBam is really expecting to read from an (indexed) bam
file with random access.

Martin

-Ryan Thompson

_______________________________________________
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

[Bioc-devel] Reading FASTQ/BAM from open file handle?

Thread (4 messages)