[prev in list] [next in list] [prev in thread] [next in thread]
List: bioc-devel
Subject: Re: [Bioc-devel] Reading FASTQ/BAM from open file handle?
From: Martin Morgan <mtmorgan () fhcrc ! org>
Date: 2012-12-05 0:37:50
Message-ID: 50BE975E.1020605 () fhcrc ! org
[Download RAW message or body]
On 12/04/2012 03:17 PM, Ryan C. Thompson wrote:
> 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@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@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[prev in list] [next in list] [prev in thread] [next in thread]
Configure |
About |
News |
Add a list |
Sponsored by KoreLogic