Closed ArtPoon closed 5 months ago
Dear @ArtPoon,
Thanks for this highly detailed issue report. The strange behavior arises because the Slatkin-Maddison analysis has been ported to use CLI keyword arguments:
hyphy % hyphy sm --help
Available analysis command line options
---------------------------------------
Use --option VALUE syntax to invoke
If a [reqired] option is not provided on the command line, the analysis will prompt for its value
[conditionally required] options may or not be required based on the values of other options
tree [required]
The Newick tree string defining the topology to use for testing
groups
The number of compartments to test
default value: 2
"description-"+(sm.i+1) [computed at run time] [required]
"Description for sequences in compartment "+(sm.i+1) [computed at run time]
"regexp-"+(sm.i+1) [computed at run time] [required]
"Regular expression to select the branches in compartment _"+sm.tag+"_" [computed at run time]
replicates
The number of bootstrap replicates
default value: 1000
weight
Probability of branch selection for structured permutation [0-1]; 0 = classical Slatkin-Maddison, 1 = fully structured
default value: 0.2
use-bootstrap
Use bootstrap weights to respect well supported clades
default value: Yes
output
Write the JSON file here (default is to save to the same path as the tree file + '_SM.json')
default value: sm.json_file [computed at run time]
In particular, the number of groups is given a default value of 2
which will be consumed in the interactive mode, unless you specify the -I
(capital eye) flag, when you call HyPhy. So, if you do hyphy -I
and then follow your workflow, then all prompts will be made.
Best, Sergei
PS You can also specify some (or all) of the analysis arguments via CLI flags, e.g.
$hyphy sm --groups 3
(the rest of the no-default-value prompts will be via `stdin`)
Wow I'm so old that I was trying to run the CLI the ancient way. Thanks for the correction :-)
Version info:
HYPHY 2.5.60(MP) for Linux on x86_64 x86 AVX SIMD with FMA3 zlib (v1.2.11) commit 6282dbbe0b1cfc6be110ca2d2ba858ab86e4df93 OS: Ubuntu 22.04.4
Steps to reproduce:
hyphy
from source directory(7) Compartmentalization
(5) Perform a classic and structured Slatkin-Maddison test for the number migrations.
tests/hbltests/UnitTests/HBLCommands/res/EU3031.nwk
when prompted for tree file.Outcome:
Analysis:
line 43 in
SM-2019.bf
According to
libv3/IOFunctions.bf
:Note
sm.leaf_count
(upper bound)) is reported as 3031. Nothing seems unusual here.Does this prompt issue arise with other scripts? No, I proceeded through
SimmondsAI.bf
without issues.Does this arise with a minimal script? I tried the following:
and obtained the following output: