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JosephCrispell / homoplasyFinder

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment
GNU General Public License v3.0
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noInconsistentSites is malformed? #6

Closed flashton2003 closed 4 years ago

flashton2003 commented 4 years ago

Hi Joe,

I just tried to read the noInconsistentSites file and it seems to be malformed. Maybe easiest if I give you the original alignment and treefile to see if it's replicable for you?

Alignment (68 Mb gzipped).

Tree.

Ta,

Phil

JosephCrispell commented 4 years ago

Hi Phil,

So it does! That is very weird, I'll fix it and let you know when I have updated the code.

Thanks for pointing this out!

Just for my reference, this is what my noInconsistentSites_DATE.fasta file looks like:

3231 3938 2031 3035 3035 360a 3e31 3634
3934 2d45 5252 3332 3536 3132 370a 4341
...

Also, this file should be called: sequences_withoutHomoplasies_DATE.fasta.

Joe

JosephCrispell commented 4 years ago

Hi Phil,

Flip, that was a tricky bug to track down. Thanks so much for pointing it out, it should be fixed now. Note that the noInconsistentSites_DATE.fasta name has been slightly changed to the following sequences_noInconsistentSites_DATE.fasta.

I have updated all versions of homoplasyFinder (command line, GUI and R package).

Let me know if it works on your end now.

Thanks!

Joe

flashton2003 commented 4 years ago

Hi Joe,

Yeah, that works well now. Thanks for the quick fix!

Phil