[Bioperl-l] sequence trace index data

[Ewan Birney]

On Thu, 19 Dec 2002, Chad Matsalla wrote:

> 
> Greetings all,
> 
> Does anybody have any opinion on how trace index points should be
> stored?
> 
> I am talking about the following situation:
> 
> 1. I have an ab1-formated trace file
> 2. I call the bases using phred
> 3. Using SeqIO, I gather the phred data from the .phd.1 file (generated
> by phred.
> 4. I pass what data into Bio::Tools::Alignment::Trim.pm and get what it
> thinks are the boundries for good sequence.
> 5. I then take a slice of the .phd.1 file and pass it into scf.pm's
> write_seq(Bio::Seq::SeqWithQuality) to generate a new scf representing
> just the good region.
> 
> 
> The problem as it stands is that phd.pm igores trace indices when it
> reads in .phd files. I can fix that easily enough (I already have) but
> the larger question is:
> Where should trace index data go?
> 
> I have placed it as an array in Bio::Seq::SeqWithQuality for now because
> I have to blow this project out the door but if anybody has better
> ideas, please let me know.


I suspect we should make a Bio::Seq::Read object and have a 
Bio::Seq::SeqWithQualityI which both Bio::Seq::SeqWithQuality (bases 
and quality values) and Bio::Seq::Read (trace file with called bases and 
trace points).


Bio::Seq::SeqWithQualityI should probably inheriet from Bio::PrimarySeqI



Whilst you are in there - any chance of you squashing bugs 1267, 1268 in 
Bugzilla?



> 
> Chad Matsalla
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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