ms to msprime conversion error (using demes.from_ms)

[mshpak76]

I have some ms scripts that I'm trying to convert to msprime using the from_ms() function in the demes package. I tried testing it on a simple example of toy code and keep getting the same error, even though I essentially followed the same format as in the example given here:

#1897

I have:

cmd = ("-I 3 5 5 5 -ej 0.25 3 2 -ej 0.75 2 1 -n 2 0.5 -n 3 0.2")
demes.from_ms(cmd, N0=10000, deme_names=None)

which gives me the error message:

TypeError: from_ms() takes 1 positional argument but 2 positional arguments (and 1 keyword-only argument)

There's evidently something subtly wrong with my syntax, though as far as I can tell my input argument format matches the example given in its format.

I have an additional question about from_ms() - rather than returning a graph, is there some way to get actual msprime code as output?

Thanks, Max

[grahamgower]

Hi @mshpak76. The error is because you need to specify the second parameter (and third) by name. So it needs to be from_ms(cmd, N0=10000) rather than from_ms(cmd, 10000). Your edited code example works for me!

[mshpak76]

Thanks, it seems to work now (at least it doesn't throw an error). As a follow-up, is there some way to see the msprime code that is generated from ms in the conversion process rather than just getting the graph object as output?

…

On Mon, Jun 13, 2022 at 9:38 AM Graham Gower ***@***.***> wrote: Hi @mshpak76 <https://github.com/mshpak76>. The error is because you need to specify the second parameter (and third) by name. So it needs to be from_ms(cmd, N0=10000) rather than from_ms(cmd, 10000). Your edited code example works for me! — Reply to this email directly, view it on GitHub <#2069 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUZMZCOGFFPAH6Q3B2OEH6LVO5BURANCNFSM5YUM5LMA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- ======================= Max Shpak, Ph.D. Department of Genetics University of Wisconsin Madison, WI 53706

[grahamgower]

The demes command line interface might be simpler in this case?

$ demes ms -N0 10000 -I 3 5 5 5 -ej 0.25 3 2 -ej 0.75 2 1 -n 2 0.5 -n 3 0.2 > model.yaml
$ cat model.yaml
time_units: generations
generation_time: 1
demes:
- name: deme1
  epochs:
  - {end_time: 0, start_size: 10000.0}
- name: deme2
  start_time: 30000.0
  ancestors: [deme1]
  epochs:
  - {end_time: 0, start_size: 5000.0}
- name: deme3
  start_time: 10000.0
  ancestors: [deme2]
  epochs:
  - {end_time: 0, start_size: 2000.0}

You can pass that file directly to msprime's command line interface

msp ancestry --demography model.yaml ...

And you can plot the yaml demography using demesdraw.

demesdraw tubes model.yaml model.svg

If you really want/need to work in Python, then you can look at the msprime.Demography object constructed via from_demes(). There's no msprime code generated here, per se. But the Demography object can be directly inspected.

import demes
import msprime

cmd = "-I 3 5 5 5 -ej 0.25 3 2 -ej 0.75 2 1 -n 2 0.5 -n 3 0.2"
graph = demes.from_ms(cmd, N0=10000)
demog = msprime.Demography.from_demes(graph)
print(demog.debug())

$ python /tmp/a.py
DemographyDebugger
╠══════════════════════════════════╗
║ Epoch[0]: [0, 1e+04) generations ║
╠══════════════════════════════════╝
╟    Populations (total=3 active=3)
║    ┌───────────────────────────────────────────────────────────────────┐
║    │       │     start│       end│growth_rate  │ deme1 │ deme2 │ deme3 │
║    ├───────────────────────────────────────────────────────────────────┤
║    │  deme1│   10000.0│   10000.0│ 0           │   0   │   0   │   0   │
║    │  deme2│    5000.0│    5000.0│ 0           │   0   │   0   │   0   │
║    │  deme3│    2000.0│    2000.0│ 0           │   0   │   0   │   0   │
║    └───────────────────────────────────────────────────────────────────┘
╟    Events @ generation 1e+04
║    ┌───────────────────────────────────────────────────────────────────────────────┐
║    │   time│type        │parameters        │effect                                 │
║    ├───────────────────────────────────────────────────────────────────────────────┤
║    │  1e+04│Population  │derived=[deme3],  │Moves all lineages from the 'deme3'    │
║    │       │Split       │ancestral=deme2   │derived population to the ancestral    │
║    │       │            │                  │'deme2' population. Also set 'deme3'   │
║    │       │            │                  │to inactive, and all migration rates   │
║    │       │            │                  │to and from the derived population to  │
║    │       │            │                  │zero.                                  │
║    └───────────────────────────────────────────────────────────────────────────────┘
╠══════════════════════════════════════╗
║ Epoch[1]: [1e+04, 3e+04) generations ║
╠══════════════════════════════════════╝
╟    Populations (total=3 active=2)
║    ┌───────────────────────────────────────────────────────────┐
║    │       │     start│       end│growth_rate  │ deme1 │ deme2 │
║    ├───────────────────────────────────────────────────────────┤
║    │  deme1│   10000.0│   10000.0│ 0           │   0   │   0   │
║    │  deme2│    5000.0│    5000.0│ 0           │   0   │   0   │
║    └───────────────────────────────────────────────────────────┘
╟    Events @ generation 3e+04
║    ┌───────────────────────────────────────────────────────────────────────────────┐
║    │   time│type        │parameters        │effect                                 │
║    ├───────────────────────────────────────────────────────────────────────────────┤
║    │  3e+04│Population  │derived=[deme2],  │Moves all lineages from the 'deme2'    │
║    │       │Split       │ancestral=deme1   │derived population to the ancestral    │
║    │       │            │                  │'deme1' population. Also set 'deme2'   │
║    │       │            │                  │to inactive, and all migration rates   │
║    │       │            │                  │to and from the derived population to  │
║    │       │            │                  │zero.                                  │
║    └───────────────────────────────────────────────────────────────────────────────┘
╠════════════════════════════════════╗
║ Epoch[2]: [3e+04, inf) generations ║
╠════════════════════════════════════╝
╟    Populations (total=3 active=1)
║    ┌───────────────────────────────────────────┐
║    │       │     start│       end│growth_rate  │
║    ├───────────────────────────────────────────┤
║    │  deme1│   10000.0│   10000.0│ 0           │
║    └───────────────────────────────────────────┘