[gt-users] some questions

Giorgio Gonnella ggonnell at yahoo.it
Sun Jul 26 22:52:37 CEST 2009


(1) About 2-3 months ago I printed a list of tools using 'gt -help'; one of them was 'gt exercise', which conversely had a long list of exercise tool. I was wondering why it is not present anymore. I am not missing anything specific, just wondering.

(2) Is there a 'tool' you may use to extract subsequences of a given lenght?

If the answer to the second question is 'no' and if it doesn't turn out to be too difficult for a complete beginner in genometools coding and almost C newbie like me, I was thinking to try taking some confidence to the project and implement such a functionality in a new tool as a first step to a basic sequencing reads simulator - I don't really need it, but I think is a simple enough thing to start with. Do you think it makes sense to do it? 

To do it I think I should: (is that right or am I missing some steps?)
- clone the repo from git://genometools.org/genometools.git
- open a new branch in my local repository
- I was thinking of taking another simple tool, for example gt_seq_filter as an example
- write my tool in a similar way / debug it 
- probably write some unit tests? are there tests for each tool?
- check that everything still compiles correctly and that tests run correctly
- when everything looks fine, ask you if would like to have a look at it for an eventual merge in the project

Giorgio


      


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