[Biococoa-dev] Even more on sequence formats

[Peter Schols]

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.
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>
>
> **************************************************************
>                         ** 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
>                       E-mail: a.griekspoor at nki.nl
>                    Web: http://www.mekentosj.com
>
> MacOS X: The power of UNIX with the simplicity of the Mac
>
> ***************************************************************
>
>
> *********************************************************
>                     ** 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
>                   E-mail: a.griekspoor at nki.nl
>               Web: http://www.mekentosj.com
>
>                             iRNAi, do you?
>              http://www.mekentosj.com/irnai
>
> *********************************************************
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm