[BioSQL-l] FW: SeqWithQuality and biosql

[Richard HOLLAND]

I'd think storing it in BioSQL as 2-byte pairs would be good. First byte
is the base (an ASCII character), second byte is the quality (an 8-bit
integer). Sure it wastes a few bits but so does normal DNA...


Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> mark.schreiber at novartis.com
> Sent: Tuesday, July 05, 2005 1:44 PM
> To: Marc Logghe
> Cc: biosql-l-bounces at portal.open-bio.org; biosql-l at open-bio.org
> Subject: Re: [BioSQL-l] FW: SeqWithQuality and biosql
> 
> 
> Hello -
> 
> I was wondering about similar issues with biojava. As you may 
> (or may not) 
> know biojava can make sequences from symbols in any alphabet, 
> two examples 
> are DNA and the integer alphabet (a collection of Symbols that are 
> integers). Biojava can also make compound alphabets, one such 
> example is 
> the Phred alphabet which is the multiplication of DNA x Integer 
> (technically a subset of Integer from 0 to 99).
> 
> Because sequence in BioSQL is stored in a CLOB if you can encode your 
> SeqWithQuality as a String of characters you can store it. 
> With the case 
> above (which is probably similar to yours) you would need 400 
> characters 
> to store it which is too large for ASCI but could be done in 
> Unicode. The 
> downside is your persitance layer needs to know how to encode 
> and decode 
> your SeqWithQuality. I'm not familiar how BioPerl would do 
> this. BioJava 
> would need to Implement a SymbolTokenizer for the alphabet and then 
> persistance would happen automatically (assuming your DB is OK with 
> Unicode). An alternative would be to make a tokenizer that 
> uses more than 
> single character tokens for encoding (eg A23 G40 T34 C22 etc).
> 
> The alternative you suggest of storing two sequences with a 
> relationship 
> is also nice (because you can retreive each part seperately) but also 
> requires your persitance layer to know about it. However, it has big 
> disadvantages because they are not strongly tied to each 
> other. If you 
> manipulate one you might invalidate the other. Also if you 
> delete one the 
> other will probably not be deleted in a cascade.
> 
> Not sure if any of this helps but a consensus on how to store 
> this kind of 
> information would be good so the bio* projects do it the same way. 
> Consensus in this case will probably mean whatever the first 
> implementation is.
> 
> - Mark
> 
> 
> 
> 
> 
> "Marc Logghe" <Marc.Logghe at devgen.com>
> Sent by: biosql-l-bounces at portal.open-bio.org
> 07/04/2005 05:56 PM
> 
>  
>         To:     <biosql-l at open-bio.org>
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [BioSQL-l] FW: SeqWithQuality and biosql
> 
> 
> Apologies for cross posting, I had picked the wrong mail adress :-(
> 
> -----Original Message-----
> From: Marc Logghe 
> Sent: Monday, July 04, 2005 11:43 AM
> To: bioperl-l at portal.open-bio.org
> Subject: SeqWithQuality and biosql
> 
> Hi all,
> I am currently exploring the possibility to store a
> Bio::Seq::SeqWithQuality object in biosql.
> Has anyone ever tried this ?
> One possibility would be to
> 1) split up the Bio::Seq::SeqWithQuality object into a plain
> Bio::Seq::RichSeq and a Bio::Seq::PrimaryQual
> 2) store them separately in biosql; different namespaces
> 3) link them with a relation term.
> 4) make a custom adaptor to fetch the persistent objects from 
> biosql and
> reconstruct the Bio::Seq::SeqWithQuality
> 
> Does that make sense ? Any other suggestions/possibilities ?
> As a test I tried to load a Bio::Seq::PrimaryQual in biosql using the
> load_seqdatabase.pl but it fails because 
> Bio::Seq::PrimaryQual does not
> have a namespace method.
> I hope I'm wrong but I have the impression there is a long 
> way to go ;-)
> 
> Marc
> 
> 
> 
> 
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