[Biococoa-dev] Even more on sequence formats

[a.griekspoor at nki.nl]

See Koen, there's the TNT already ;-)
Peter any change the beast is also in there, that would alleviate you from any claims coming from Koen..
Cheers,
Alex

Ps. Peter good luck dealing with the burglary, sorry to hear that.


-----Original Message-----
From:	Peter Schols [mailto:peter.schols at bio.kuleuven.be]
Sent:	Tue 4/11/2006 3:08 PM
To:	Alexander Griekspoor
Cc:	biococoa-dev at bioinformatics.org
Subject:	Re: [Biococoa-dev] Even more on sequence formats

ReadSeq could be a good example indeed.
I guess we have most of them, except for IG, NBRF, Fitch, Zuker,  
Olsen, ASN.1.
We do have Clustal, Nona, TNT, Hennig, PDB however ;-)
(PAUP == Nexus).

Peter




> Finally, to come back to the question on the formats, perhaps we  
> can learn from a classic sequence reader package called ReadSeq by  
> d.g.gilbert.
> It reads the following formats, which are outlined in the Formats  
> textfile inside the src folder:
>          1. IG/Stanford           10. Olsen (in-only)
>          2. GenBank/GB            11. Phylip3.2
>          3. NBRF                  12. Phylip
>          4. EMBL                  13. Plain/Raw
>          5. GCG                   14. PIR/CODATA
>          6. DNAStrider            15. MSF
>          7. Fitch                 16. ASN.1
>          8. Pearson/Fasta         17. PAUP
>          9. Zuker (in-only)       18. Pretty (out-only)
>
> Some of them we support, but some not, so we can even add a few  
> formats, plus the source code nicely shows how to discriminate them.
> The latest version switched from c to java and added even a few  
> more formats, so there's plenty to add ;-) The source also contains  
> many sample files for testing purposes.
> I'm not sure where it can be found nowadays, so I put it  
> temporarily on our server for you guys to download:
> http://www.mekentosj.com/temporary/readseq.zip
> Have a look at it and tell me what you think.
> Cheers,
> Alex
>
>
>> For those who feel like helping out, the way to implement the code  
>> is:
>>
>> - remove white lines (optional)
>> - get each line
>> - extract annotations into a BCAnnotationsArray
>> - extract the sequence(s) into an NSString
>> - once done with all the sequences, create a BCSequence from each  
>> sequenceString
>> - add the annotations to each BCSequence
>> - add the new BCSequence(s) to the BCSequenceArray
>> - return the BCSequenceArray
>>
>>
>> cheers,
>>
>> - Koen.
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>>
>
> **************************************************************
>                         ** Alexander Griekspoor **
> **************************************************************
>                  The Netherlands Cancer Institute
>                  Department of Tumorbiology (H4)
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>
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> ***************************************************************
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>
> *********************************************************
>                     ** Alexander Griekspoor **
> *********************************************************
>               The Netherlands Cancer Institute
>               Department of Tumorbiology (H4)
>          Plesmanlaan 121, 1066 CX, Amsterdam
>                   Tel:  + 31 20 - 512 2023
>                   Fax:  + 31 20 - 512 2029
>                   AIM: mekentosj at mac.com
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