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HYPHY 2.5.60(MP) for Linux on x86_64 x86 AVX SIMD with FMA3 zlib (v1.2.11)
commit 6282dbb
OS: Ubuntu 22.04.4
Steps to reproduce:
Launch hyphy from source directory
Select (7) Compartmentalization
Select (5) Perform a classic and structured Slatkin-Maddison test for the number migrations.
Enter tests/hbltests/UnitTests/HBLCommands/res/EU3031.nwk when prompted for tree file.
Outcome:
interface bypasses user prompt for number of groups, defaulting to 2, and proceeds directly to identification of group 1.
>How many branch classes are there (permissible range = [2,3031], default value = 2, integer): groups: 2
>Please provide a description for group of branches 1 :
Analysis:
line 43 in SM-2019.bf
sm.group_count=io.PromptUser(">How many branch classes are there", 2, 2, sm.leaf_count, TRUE);
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:
LoadFunctionLibrary ("libv3/IOFunctions.bf");
leaf_count=10;
group_count=io.PromptUser(">How many branch classes are there", 2, 2, leaf_count, TRUE);
fprintf(stdout, group_count, "\n");
and obtained the following output:
art@Peregrine:~/git/hyphy/res/TemplateBatchFiles$ hyphy test.bf>How many branch classes are there (permissible range = [2,10], default value = 2, integer): 55
The text was updated successfully, but these errors were encountered:
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`)
Version info:
HYPHY 2.5.60(MP) for Linux on x86_64 x86 AVX SIMD with FMA3 zlib (v1.2.11)
commit 6282dbb
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:
The text was updated successfully, but these errors were encountered: