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informative codons method for kaks -- Bio/Align/DNAStatistics.pm #14

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Albert Vilella (Albert Vilella) Original Redmine Issue: 2078, https://redmine.open-bio.org/issues/2078 Original Date: 2006-08-17 Original Assignee: Bioperl Guts

I think it would be nice to have a method in Bio/Align/DNAStatistics.pm that gives the number of informative codons for kaks in a MSA. That is, the codons that are used in the calculation of kaks. This, AFAIK, more or less what codeml calls “patterns”.

I often find myself in the situation of wanting to know how big is the CDS alignment not in terms of sequence length, but of the number of codons that are going to be used in the kaks statistics. I guess this method would help in that.

The method could:

return the number of informative codons? maybe return a new seqarray with only the informative codons?

What you reckon? Jason? Chris?

cjfields commented 8 years ago

Original Redmine Comment Author Name: Chris Fields Original Date: 2006-08-17T10:22:03Z

Don’t forget Sendu!

As long as the method is valid for the class (which it is) and there are tests added for it, sure why not!

cjfields commented 8 years ago

Original Redmine Comment Author Name: Sendu Bala Original Date: 2006-09-02T12:23:27Z

Are you interested in adding this yourself Albert?

cjfields commented 7 years ago

@avilella still interested in this?