Closed Cactusolo closed 3 years ago
Sorry for the trouble. That version is a bit old (latest release is v1.2.1, and the master branch is v1.3). So please try upgrading. If it still fails, please provide input that we can troubleshoot.
@josephwb it resolved after upgrade to v.1.3. Many thanks!
One small comment that, I found that the tip names in the output tree file containing single quote [ ' ], which may cause problem for downstream tip manipulation. For example, it won't work for relabel the tips, unless I remove all the single quote [don't have this my original tree file], or providing correspond name mapping file with tips in single quote.
Hrm could you please provide an example (input, output, and example of a problematic label)? Quotes are only ever introduced if a label contains a newick-illegal character. But such labels should (almost) always have 2 quotes.
Hrm could you please provide an example (input, output, and example of a problematic label)? Quotes are only ever introduced if a label contains a newick-illegal character. But such labels should (almost) always have 2 quotes.
# original tree
[cactus@test]$ cat test.tre
(454434-az:0.00225757676750129024,((4288:0.00095317223035216254,1197917:0.00000100000050002909):0.08510136778879195951,454421-az:0.00608116695325890220):0.00528080745550952267,454597-az:0.00112679728728448366):0.0;
# stdout output
[cactus@test]$ pxrr -t test.tre -g 1197917,4288
((4288:0.0009531722303522,1197917:0.0000010000005):0.042550683894396,('454421-az':0.0060811669532589,('454434-az':0.0022575767675013,'454597-az':0.0011267972872845):0.0052808074555095):0.042550683894396);
# output to a `test_out.tre` file
[cactus@test]$ pxrr -t RAxML_bestTree.Vahliales_2run -g 1197917,4288 -o test_out.tre
# single quote remains
[cactus@test]$ cat test_out.tre
((4288:0.0009531722303522,1197917:0.0000010000005):0.042550683894396,('454421-az':0.0060811669532589,('454434-az':0.0022575767675013,'454597-az':0.0011267972872845):0.0052808074555095):0.042550683894396);
#original tips
[cactus@test]$ pxlstr -t test.tre -i
1197917
4288
454421-az
454434-az
454597-az
Thanks for that. ATM we are quoting any label that contains a non-compliant Nexus character. -
happens to be illegal for Nexus, but not for newick. I see your point about matching labels downstream. I will figure out how to handle things more accurately.
@Cactusolo Ok things should work for you now. I may take out the compliancy-quoting, since almost no users will be aware of which characters are illegal.
FWIW:
nexus_illegal = ()[]{}/\,;:=*'"`+-<>
newick_illegal = ()[]\':;,
I have two issues with
pxrmt
function:When outgroup more than one, then raising "Segmentation fault (core dumped)"
Output to a file failed and always STOUT
The tree file was print to terminal screen and out file "test.tre" is empty. and I also tried with redirect
>test.tre
also empty.Please help and me know if you need a test data. Not sure, if I need to update to the recent version, current is v1.1.0.
Thanks!
Miao