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Extension of Orange Widgets with Dos command programs

A place to ask questions about methods in Orange and how they are used and other general support.

Extension of Orange Widgets with Dos command programs

Postby Dos2Orange » Thu Jan 13, 2005 2:49

I would like to request for a documentation that illustrates how to build an Orange Widget that wraps a dos command program. For example, a widget that converts the input data into a temp input file, and then execute a dos command program to work on the temp input file to generate a temp output file. The widget then read in and parse the temp output file into a standard data structure, before piping the data to the downstream widgets, all temp files (input and output) are deleted.

One possible application is bioinformatics open source program e.g. EMBOSS. The parameters for the input and output interface of each of the programs are well defined.
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/index.html

Emboss for windows
http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html

Workflow using EMBOSS: Taverna
http://taverna.sourceforge.net/docs/tutorial/TavernaTutorial.htm

Postby Blaz » Thu Jan 13, 2005 8:50

I understand what you would like to do with widgets, and what you ask should be quite simple to program. But running things from dos, piping, parsing, etc., is nothing about widgets but about python programming. You should be able to easily find the documentation which you are requesting within Python stadard documentation.

Wizard to import a list of dos command programs

Postby Dos2Orange » Thu Jan 13, 2005 21:13

First, I just started learning Python. Second, I wish this feasture is incorporated as a Wizard that begniner user is able to run through the Wizard, to define the location of the dos program, the parameter of the input and the data structure of the input and output for the dos program. Third, I hope this mail will generate interest among competent python programmers in this forum who are also interested to implement sequence analysis based on EMBOSS to Orange.


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