[Bioperl-l] need info

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Nov 18 01:53:58 EST 2005


Like Barry said, familiarizing yourself with bioperl is the first thing to do.
Most of people have per project s that they pursue. I am sure you will come up 
with one in due time.

Here is one area that needs a lot of help. Although, we have a huge collection 
of tests, there are still modules with no tests at all. We'd like to test at 
least all public methods. Look for examples in the t directory of bioperl.

A more computer science related problem is to identify classes that do not 
have tests. There are quite a few tightly linked clusters of classes that 
that do not make sense to tests individually, like SearchIO modules related 
to BLAST/FASTA parsing. The problem is to identify those modules. At some 
point I tried to scan through all test files and compare that to the list of 
classes produced by the maintenance/modules.pl script to identify the ones in 
need of testing but got so many false positives, that I moved on to other 

If you, or anyone, could create a script, e.g. maintenance/needtesting.pl, 
that would do that task, it would be a big step ahead.

A way to do it would be take the code in maintenance/modules.pl that creates a 
hash of modules and their immediate parents, scan the t/*.t files to see 
which modules are being tested, follow the inheritance of path of every 
module and check which modules within Bio namespace they 'use', and mark all 
those a tested, and finally print out a list of untested modules.



On Thursday 17 November 2005 21:04, kumail wrote:
> dear sir
> i am niraj shrestha from Nepal. currently i am teaching at Kathmandu
> University. i am graduated from the university in 2001 in computer science
> & engineering. my research interest is in bioinformatics, parallel and
> distributed network, semantic web. so if i can help or can do some work for
> bio-pearl then i am ready for that. looking forward to your kind
> suggestions.
> with regards,
> _____________________________________
> Niraj Shrestha
> Department of Computer Science & Engineering
> Kathmandu University,
> Dhulikhel, Nepal
> P.O.Box: 6250, Kathmandu, Nepal
> email: niraj at ku.edu.np, niraj_sh at hotmail.com, niraj_sh at yahoo.com
> website: http://ku.edu.np/~niraj
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of the Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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