[Bioperl-pipeline] new pipeline

[Shawn Hoon]

> Hello,
>
> I am a student of computer science and I intern at the working group  
> of Stefan Rensing (www.plant-biotech.net, Germany, Freiburg,  
> University, Faculty of Biology).
>
> My task is to build a new pipeline with Biopipe:
> - runs in local mode
> - blast FASTA files against a intern database.
> - blast results again a database.
> - store results in a MySQL database, so we can easily export outputs  
> to a spreadsheet. Or as a alternativ directly store the results in a  
> self-defined spreadsheet.
>
>
> I did not find an example pipeline, which parses the blast output to a  
> database. Will Biopipe do this for me ?
> And in general: Which converting of formats is possible with the  
> current Biopipe?
> Do I have to write new methods in perl also?
>


The format conversion of file formats is not done by Biopipe. Instead,  
it generalizes by allowing different Input and Output modules( called  
iohandlers) to be
used to interface the inputs and outputs of analysis between databases  
and files. The most comprehensive set of perl modules that allow these  
are from bioperl. For example:
Bio::SeqIO, Bio::AlignIO, Bio::TreeIO etc, these all may be used by  
Biopipe via the xml definition of the pipeline. Most of the time you  
will use this as the analysis modules (called runnables)
return mostly bioperl objects.You can also write to mySQL if you have  
the appropriate
adaptor modules that are able to take the output objects and calling  
the appropriate sql to store the data. If you have your own schema, you  
must write your own adaptor
See the examples mentioned by kiran for examples.

cheers,


shawn

> Many question, I am glad to hear from you.
>
>
> Regards
> Joachim Strach
>
>
> -- Joachim H. Strach
> Phone in office from 9.00 am to 5 pm:
> Germany 0761-203-6988
> _______________________________________________________________________ 
> _______
> Doppelsieg fur WEB.DE FreeMail und Club bei Stiftung Warentest!
> Beste Sicherheitswertung und Verfuegbarkeit! http://f.web.de/?mc=021181
>
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline at bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>
>