[BioC] ShortReadQ constructor

[Ivan Gregoretti]

Hi Marcus,

Actually, I originally tried using the method (if it existed) to
update the ids but got the error that you show above.

By the way, going through my records I found that indeed I had a typo.
I meant to write ShortReadQ() but I wrote ShortRead(). No wonder it
complained about not having a slot for quality.

Thank you,


Ivan

Ivan Gregoretti, PhD
Bioinformatics




On Mon, Oct 7, 2013 at 11:24 PM, Marcus Davy <mdavy86 at gmail.com> wrote:
> It doesn't look like a method has been written to update the id slot, direct
> access does work, I also think using renew() is nicer.
>
> try(id(srq1) <- paste(id(srq1), 'tested'))
> Error in id(srq1) <- paste(id(srq1), "tested") :
>   could not find function "id<-"
>
> ## Direct injection -probably not recommended
> srq1 at id <- BStringSet( paste(id(srq1), 'tested'))
>
> renew() also catches enforced structure between 'sread' and 'quality', e.g.
>
>  try(renew(srq1, quality=FastqQuality(c("HH","H"))))
> Error in validObject(.Object) :
>   invalid class "ShortReadQ" object: some sread and quality widths differ
>
> I have also had cause to update ids in a ShortReadQ object, in my case for
> input into a Short read aligner, useful additional auxiliary information can
> go into the QNAME field of a bam file.
>
> cheers,
>
> Marcus
>
>
>
>
> On Tue, Oct 8, 2013 at 1:44 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>>
>> The renew() looks really handy. The direct use of the constructor is
>> something that I tried but failed to me. I probably had one of those
>> invisible typos.
>>
>> Thank you.
>>
>> Ivan
>>
>>
>> Ivan Gregoretti, PhD
>> Bioinformatics
>> Cell Signaling Technology, Inc
>> 3 Trask Lane
>> Danvers, MA 01923. USA.
>> Phone +1-978-867-2429
>>
>>
>> On Mon, Oct 7, 2013 at 8:31 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>> > On 10/07/2013 05:06 PM, Ivan Gregoretti wrote:
>> >>
>> >> Hello Martin,
>> >>
>> >> Great. So,
>> >>
>> >> srq1 <- ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")),
>> >> FastqQuality(c("HHHH", "HHHHHHH")), BStringSet(c("read1", "read2")))
>> >>
>> >> gets me what I wanted. Now I have a part two to my question:
>> >>
>> >> How do I modify srq1's id?
>> >>
>> >> For instance, id(srq1) produces
>> >>
>> >>> id(srq1)
>> >>
>> >>    A BStringSet instance of length 2
>> >>      width seq
>> >> [1]     5 read1
>> >> [2]     5 read2
>> >>
>> >> but I want to modify srq1's id so that it looks like this
>> >>
>> >>> BStringSet(paste(id(srq1), 'tested'))
>> >>
>> >>    A BStringSet instance of length 2
>> >>      width seq
>> >> [1]    12 read1 tested
>> >> [2]    12 read2 tested
>> >>
>> >> Please note that I intend not to construct a new instance by passing
>> >> FastqQuality(c("HHHH", "HHHHHHH")) and DNAStringSet(c("ACGT",
>> >> "GGGGACT")). I intend to copy srq1 to srq2 and then modify srq2.
>> >>
>> >
>> > ShortRead explored the notion of a 'renw'able instance, see ?renew and
>> >
>> >   srq2 = renew(srq1, id=BStringSet(paste(id(srq1), "tested")))
>> >
>> > this
>> >
>> >   ShortReadQ(sread(srq1), quality(srq1), BStringSet(paste(id(srq1),
>> > "tested")))
>> >
>> > also works
>> >
>> > Martin
>> >
>> >
>> >> Alternatively, may I construct a new instance by passing
>> >> BStringSet(paste(id(srq1), 'tested')), sread(srq1) and quality(srq1)?
>> >> I tried by the constructor complained vociferously when I passed
>> >> quality=quality(srq1).
>> >>
>> >> Thank you,
>> >>
>> >> Ivan
>> >>
>> >>
>> >>
>> >>
>> >> Ivan Gregoretti, PhD
>> >> Bioinformatics
>> >>
>> >>
>> >>
>> >>
>> >> On Mon, Oct 7, 2013 at 3:44 PM, Martin Morgan <mtmorgan at fhcrc.org>
>> >> wrote:
>> >>>
>> >>> On 10/07/2013 12:28 PM, Ivan Gregoretti wrote:
>> >>>>
>> >>>>
>> >>>> Hello,
>> >>>>
>> >>>> Could somebody show an example of constructing a ShortReadQ object
>> >>>> instance? I can't find an example in the documentation.
>> >>>>
>> >>>>
>> >>>> For example, lets say that I have two records with the following ids,
>> >>>> sequences, and Phred qualities
>> >>>>
>> >>>> c("read1", "read2")
>> >>>> c("ACGT", "GGGGACT")
>> >>>> c("HHHH", "HHHHHHH")
>> >>>>
>> >>>> How would you now construct the ShortReadQ instance?
>> >>>
>> >>>
>> >>>
>> >>> Hi Ivan
>> >>>
>> >>> ShortReadQ(DNAStringSet(c("ACGT", "GGGGACT")),
>> >>>      FastqQuality(c("HHHH", "HHHHHHH")),
>> >>>      BStringSet(c("read1", "read2")))
>> >>>
>> >>> Martin
>> >>>
>> >>>>
>> >>>> Thank you,
>> >>>>
>> >>>> Ivan
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> Ivan Gregoretti, PhD
>> >>>> Bioinformatics
>> >>>>
>> >>>> _______________________________________________
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>> >>>>
>> >>>
>> >>>
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>> >
>> >
>> >
>> > --
>> > 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
>>
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