dear Martin:
 thank you for your help on the some codiing.
but i have a question about the function

as(quality(reads), "numeric")

the function quality must automatically identify the score system, phred+33
and phred+64.

that is good on some cases, but if i processed the data in chunk.
maybe a chunk of data have the scores above 59, but they are phred+33
i am afraid it will lead a wronge identification

can i set a parameter to tell the function as(quality(reads), "numeric") ,
the score sys is
phred+33 or 64

thank you
shan



On Tue, May 20, 2014 at 1:23 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 05/19/2014 06:49 AM, Wang Peter wrote:
>
>> i am sorry, i have another question about the coding
>>    phred64 = rawToChar(as.raw(64:104))
>>    phred33 = rawToChar(as.raw(33:73))
>> qual = chartr(phred64, phred33, quality(quality(reads)))
>> how did it deal with quality score from 59 to 63?
>>
>
> I did not include them; expand the phred64 and phred33 strings to reflect
> the desired mapping.
>
> Martin
>
>
>>
>> On Mon, May 19, 2014 at 9:32 PM, Wang Peter <wng.peter@gmail.com
>> <mailto:wng.peter@gmail.com>> wrote:
>>
>>     thank you very much
>>     you coding is so beautiful, mine is ugly
>>
>>
>>     On Mon, May 19, 2014 at 8:03 PM, Martin Morgan <mtmorgan@fhcrc.org
>>     <mailto:mtmorgan@fhcrc.org>> wrote:
>>
>>         On 05/14/2014 02:56 PM, Wang Peter wrote:
>>
>>             i worte a program to automatically dectect the scoring system
>> in
>>             fastq file
>>             and if pred+64, it should be changed into pred+33
>>
>>
>>         I would make the relevant alphabets
>>
>>            phred64 = rawToChar(as.raw(64:104))
>>            phred33 = rawToChar(as.raw(33:73))
>>
>>         translate the character representation of the underling BStringSet
>>
>>            qual = chartr(phred64, phred33, quality(quality(reads)))
>>
>>         and tag the result as phred+33
>>
>>            ShortReadQ(sread(reads), FastqQuality(qual))
>>
>>         To get a numeric representation of the quality encoding, I would
>>
>>            as(quality(reads), "numeric")
>>
>>         or for a rectangular, NA-padded representation
>>
>>            as(quality(reads), "matrix")
>>
>>         Martin
>>
>>
>>             please help me make sure it is right
>>
>>             rm(list=ls())
>>             fastqfile="1.fastq";
>>             working_dir="d:/working_dir"
>>             setwd(working_dir)
>>             library(ShortRead);
>>             reads <- readFastq(fastqfile);
>>             seqs <- sread(reads);
>>             score_sys = data.class(quality(reads));
>>             cat("the quality score system
>>             (SFastqQuality=Phred+64,__FastqQuality=Phred+33)
>> is",score_sys,"\n")
>>
>>             raw_len <- max(width(reads));
>>
>>             qual <- quality(quality(reads));
>>             myqual_16L <- charToRaw(as.character(unlist(__qual)));
>>
>>             if(score_sys =="FastqQuality")
>>             {
>>                myqual_10L <- strtoi(myqual_16L,16L)-33;   # this is for
>> other use
>>             }
>>
>>             if(score_sys =="SFastqQuality")
>>             {
>>                myqual_10L <- strtoi(myqual_16L,16L)-64;
>>                qual_temp <- PhredQuality (as.integer(myqual_10L));
>>                qual <- BStringSet(unlist(qual_temp), start= seq(from = 1,
>> to =
>>             raw_len*(length(reads)-1)+1, by = raw_len), width=raw_len);
>>
>>             }
>>             reads <- ShortReadQ(sread=seqs, quality=qual ) );
>>
>>
>>
>>         --
>>         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 <tel:%28206%29%20667-2793>
>>
>>
>>
>>
>>
>>     --
>>     shan gao
>>     Room 231(Dr.Fei lab)
>>     Boyce Thompson Institute for Plant Research
>>     Cornell University
>>     Tower Road, Ithaca, NY 14853-1801
>>     Office phone: 1-607-254-1267 <tel:1-607-254-1267>(day)
>>     Official email:sg839@cornell.edu <mailto:email%3Asg839@cornell.edu>
>>
>>     Facebook:http://www.facebook.com/profile.php?id=100001986532253
>>
>>
>>
>>
>> --
>> shan gao
>> Room 231(Dr.Fei lab)
>> Boyce Thompson Institute for Plant Research
>> Cornell University
>> Tower Road, Ithaca, NY 14853-1801
>> Office phone: 1-607-254-1267(day)
>> Official email:sg839@cornell.edu <mailto:email%3Asg839@cornell.edu>
>> Facebook:http://www.facebook.com/profile.php?id=100001986532253
>>
>
>
> --
> 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
>



-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839@cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253

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