[Bioc-sig-seq] readAligned in ShortRead package

[Ingunn Berget]

Thanks this worked well!

Ingunn
>-----Original Message-----
>From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
>Sent: Tuesday, August 04, 2009 5:45 PM
>To: Ingunn Berget
>Cc: bioC
>Subject: Re: [Bioc-sig-seq] readAligned in ShortRead package
>
>Martin Morgan wrote:
>> Ingunn Berget wrote:
>>> Dear All
>>>
>>> According to the documentation for "readAligned" in package
>"ShortRead" (version 1.2.1) the match contig column is ignored, is there
>any easy way of getting this information into R?
>>
>> as a work-around, these are text files and you might try
>>
>> ## read
>> aln <- readAligned(path_to_file, type="SolexaExport")
>> what <- rep(list(NULL), 22)
>> what[[8]] <- "character"
>> contig <- scan(path_to_file, what=what, sep="\t", fill=TRUE)[[8]]
>
>oops! quotes in quality strings will mess up parsing, and we're after
>column 12. So this should be
>
>what[[12]] <- character()
>contig <- scan(path_to_file, what=what, sep="\t",
>                fill=TRUE, quote="")[[12]]
>
>> ## check contig for correct values
>>
>> ## add to alignData
>> adata <- alignData(aln)
>> adata[["contig", labelDescription="Solexa export 'contig' data"]] <-
>>   contig
>>
>> ## update AlignedRead
>> aln <- initialize(aln, alignData=adata)
>>
>> If the files are gz-compressed, then I think you'll want to
>>
>> contig <- scan(gzfile(path_to_file), what=what, sep="\t",
>>                fill=TRUE)[[8]]
>>
>> I will update ShortRead to parse this data into alignData.
>>
>> Martin
>>
>>>
>>> Best regards
>>> Ingunn
>>>
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>>
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>
>
>--
>Martin Morgan
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>
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