Hashes in filenames cause name match issues about fastbaps

[gtonkinhill]

Hi John,

I'm having trouble reproducing the behaviour. When I run the script locally it seems to keep the '#'. I've attached the example inputs I am using. Do these work on your system?

Rscript run_fastbaps -i test.fasta -o test_fastbaps.txt -l 2 --phylogeny=test.tree -t 2

Gives

head test_fastbaps.txt
Isolates,Level 1,Level 2
1#1,9,23
2#2,9,23
3#3,9,23
4#4,3,6
5#5,9,27
6#6,9,27
7#7,9,27
8#8,3,5
9#9,2,4

test_data.zip

[johnlees]

Hi Gerry,
Ah really sorry, I think I may have got it wrong where in our pipeline this was happening. I actually think it was the iq-tree output being renamed in this way, which meant the names between the alignment and tree no longer matched (but this gave an error in fastbaps I didn't check properly, as it was actually an input issue). Sorry for wasting time!!