[Bioperl-pipeline] new pipeline

[Kiran Kumar]

Hi Joachim,
Look at the examples in /xml/examples/xml/
blast_biosql_pipeline.xml
blast_db_flat.xml

The first one reads the inputs to the blast from biosql database and
writes the output to biosql. The second one can dump to a gff format file.

Kiran

On Tue, 16 Sep 2003, Joachim H. Strach wrote:

>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?
>
>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
>