pxaa2cdn -r not working as expected

[NatJWalker-Hale]

pxaa2cdn -r not working as expected

[NatJWalker-Hale]

Having a peek, I think (though could be wrong), that this is because there is no check for -r while checking for the mismatch of lengths. I guess that will have to check if they're off by one if -r is invoked. I'll try fiddle with it my end and submit a PR if it works, unless you get to it first.

[josephwb]

Can confirm. Sorry about that. I will have a look later today. It should take a few minutes, but I am heading out the door.

[josephwb]

Ok I see what is going on. Be back soon.

[josephwb]

Should be fixed with 9f15c7a

[josephwb]

Sorry I missed your PR. I think mine works well (will put in a few tests). Yours looks fine if you can assume all files are what they say they are (nuc and associated pep). If you've somehow mixed up files, your fix will allow the program to proceed (i.e., counts are explicitly set to be equal), but would crash if the lengths are not what they should be (say, a nuc alignment shorter than the peptide on). Just thinking of ways people can break things (>ᴗ•)

[NatJWalker-Hale]

That works! Although I note that it makes the codon count in the error message for mismatching lengths off by one, e.g.

test2.cds.fa.txt

pxaa2cdn -r -a test.pep.fa.txt -n test2.cds.fa.txt
Error: for taxon '1' nucleotide alignment involves 4 codons, but protein alignment involves 2 amino acids. Skipping.
Error: for taxon '2' nucleotide alignment involves 4 codons, but protein alignment involves 2 amino acids. Skipping.

But test2.cds.fa.txt has 5 codons, etc...

Anyway, I see what you mean about my PR, will close it! Many thanks for dealing with it so quickly.

[josephwb]

Erg yes I'll fix the warning.

[NatJWalker-Hale]

legend, thanks!