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mscook / SeqFindR

A tool to easily create informative genomic feature plots
http://mscook.github.io/SeqFindR/
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Protein searches #3

Closed bawee closed 10 years ago

bawee commented 11 years ago

A tblastx and tblastn option would be handy to detect more divergent homologs.

Thanks, Mitch, such a handy tool!

happykhan commented 11 years ago

Available in my fork. (see my repos) tblastn functionality only .

mscook commented 11 years ago

@bawee: (as per your request). It will be activated soon.

happykhan commented 11 years ago

tblastx functionality added on my fork. use -X flag to trigger. See USAGE for deets.

https://github.com/happykhan/SeqFindR

bawee commented 11 years ago

Thanks Nabil and Mitch, exactly what i needed. Beers on me tomorrow at the game, if we're going somewhere.

On 16/07/2013, at 3:09 PM, Mitchell J Stanton-Cook wrote:

@bawee: (as per your request). It will be activated soon.

— Reply to this email directly or view it on GitHub.

bawee commented 11 years ago

Using -X gives this error message at the very end of the run but still produces an expected output:

/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/matplotlib/axes.py:2757: UserWarning: Attempting to set identical bottom==top results in singular transformations; automatically expanding. bottom=0, top=0.0 + 'bottom=%s, top=%s') % (bottom, top)) Trying to get config option that does not exist.

bawee commented 11 years ago

Also, is there a way to regenerate the clustering with a different identity/evalue/score cutoff without having to rerun tblastx?

mscook commented 10 years ago

I think the original issue has been addressed. Regeneration has been Hamza's work. An unchecked version is in the development branch. @bawee: if any of the further issues (i.e. comment number 3, please open a new issue).