simupop-list — A forward-time population genetics simulation environment.

[simuPOP-list] simuPOP on Apple M2

[Sid H. <si...@da...>]

Hi

I was just wondering whether anybody had managed to install simuPOP on
Apple M2. I've tried conda (not available) and building directly (C++
compilation issues) but haven't had any luck with it.

Any pointers would be much appreciated.

Thanks
Sid

[simuPOP-list] simuPOP import error

[Louise M. <lou...@gm...>]

Hi,
I just installed simuPOP on Windows 10 Pro 22H2 with Anaconda 3 using

conda install -c conda-forge simuPOP

and then I tried to run a script that contained the single command

import simuPOP

and I got the following error:

Traceback (most recent call last):
  File
"C:\ProgramData\miniconda3\Lib\site-packages\simuPOP\simuPOP_std.py", line
18, in swig_import_helper
    return importlib.import_module(mname)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\miniconda3\Lib\importlib\__init__.py", line 90, in
import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1387, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1360, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1324, in
_find_and_load_unlocked
ModuleNotFoundError: No module named 'simuPOP._simuPOP_std'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\LFM\Dropbox\Clustering\St_Andrews\simupop_import.py", line
1, in <module>
    import simuPOP as sim
  File "C:\ProgramData\miniconda3\Lib\site-packages\simuPOP\__init__.py",
line 323, in <module>
    from simuPOP.simuPOP_std import *
  File
"C:\ProgramData\miniconda3\Lib\site-packages\simuPOP\simuPOP_std.py", line
21, in <module>
    _simuPOP_std = swig_import_helper()
                   ^^^^^^^^^^^^^^^^^^^^
  File
"C:\ProgramData\miniconda3\Lib\site-packages\simuPOP\simuPOP_std.py", line
20, in swig_import_helper
    return importlib.import_module('_simuPOP_std')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\miniconda3\Lib\importlib\__init__.py", line 90, in
import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named '_simuPOP_std'

What can I do to fix this? Thanks very much.

Louise

[simuPOP-list] Wright Fisher Forward Simulation

[Nihara De S. <suh...@gm...>]

Hi all,
Highly appreciate if you could clarify whether below is supported in
simuPop. The Wright Fisher forward simulation for generations from 2,8,
giving effective population value, mutation rate, no of loci, individuals
with diploid structure and a minimum allele frequency value and get
population as output in genepop format?

Thanks in advance

[simuPOP-list] Forward simulation of DNA recombination from 16 defined individual ancestor

[Neil M. <nei...@gm...>]

Because of the simplicity of my intended modeling, I fear that using a robust program like simuPOP might be like swatting a fly with a hammer.

My hope is that by using the program, I can gradually increase the complexity of my models, and so want to use simuPOP at the outset.

I am working on a genealogy matrix derived from downstream recombination of DNA segments.  I intend to ignore any consideration of mutations or variations in recombination rates across the chromosomal board.  

By example, I will start with a population of 16 defined ancestors, designating their two respective paired maternal and paternal chromosome sequences something like ‘AAAAAAAAAAAA’  — ‘aaaaaaaaaaaa’  through ‘PPPPPPPPPPPP’ — ‘pppppppppppp' (of course much longer)

The first generation offspring of A and B, might have recombinant sequences that look like  'AAAaaaAAaaaaa’ and ‘bbbbbbbbbBBBBb’ randomly recombined without attempting variations across the chromosomal map.  I would like to simulate recombination rates per million and be able to adjust this in different simulations.

Future generations will each contribute to a cascade of descendents, each of which will have a decreasing component of their respective direct original 16 ancestors.  External DNA contributions, increasing with each generation, can simply be designated as ‘Z’ as they will not be considered in the intended analysis.

My goal is to model the frequency of cross-matched segments in descendant generations, and compare it with known human DNA segment match data. 

My first line goal is to develop multiple instances of grouped match triangulations datasets, and analyze them with respect to known and defined relationships among the entire descendant population.

Is this something that seems appropriate for this software, and could you gently poke me toward the correct way to achieve this ?

Thank you in advance for your consideration and help

Neil Millikin
(retired scientist with an interest in applying computer science to genetic genealogical analysis)

I am quite proficient with Python data analysis, but freely admit to getting lost when reading the source code.

[simuPOP-list] Assigning offspring infofield independently from parents infofield

[Joane E. <joa...@al...>]

Hello,
I have several subpopulations. I'd like to set up one infofield that would represent the subpopulation where the individual was born (the infofield is called 'origin'). It seems to me that during-mating taggers only allow to assign infofields to offspring based on parents' infofields, not something independent from parents (like the subpopulation of birth).

Alternatively I found a way to add the information right after reproduction using Infoexec, but with 12 subpopulations it looks bulky and inefficient:

postOps=[
            sim.InfoExec('origin=0', subPops=[(0,0)]),
            sim.InfoExec('origin=1', subPops=[(1,0)]),
            sim.InfoExec('origin=2', subPops=[(2,0)]),
            sim.InfoExec('origin=3', subPops=[(3,0)]),
            sim.InfoExec('origin=4', subPops=[(4,0)]),
            sim.InfoExec('origin=5', subPops=[(5,0)]),
            sim.InfoExec('origin=6', subPops=[(6,0)]),
            sim.InfoExec('origin=7', subPops=[(7,0)]),
            sim.InfoExec('origin=8', subPops=[(8,0)]),
            sim.InfoExec('origin=9', subPops=[(9,0)]),
            sim.InfoExec('origin=10', subPops=[(10,0)]),
            sim.InfoExec('origin=11', subPops=[(11,0)]),

(By the way, all subpopulations are age-structured and virtual subpopulation 0 correspond to the newborns)

Is there a 1-line solution that I overlooked?

Thank you!

Joane Elleouet

[simuPOP-list] varPlotter (simuPOP.plotter)

[Natasha S. <nat...@gm...>]

Hi Everyone,

I was wondering if the module simuPOP.plotter still exists?

If not, do you have any alternatives on how to generate graphs within
Python?

Thank you,
Natasha

[simuPOP-list] ParentsTagger() affecting defdict?

[Natalie C L. <ncl...@uw...>]

Hello,

I'm trying to calculate multiple statistics using the Stat operator, as
well as tag parents. When I include the ParentsTagger() operator, it seems
to prevent the defdict from storing stats. From the reference manual, I
can't seem to understand how the ParentsTagger() is influencing the Stats
operator. Do you know why this is happening? Please see my code below,
where I print the allele frequencies of the first locus from the first
subpop in each generation from the defdict, without and with the
ParentsTagger().

Thank you,

Natalie Lowell
Graduate Student, Hauser Lab
School of Aquatic and Fishery Sciences
University of Washington
(760) 420-2281 | ncl...@uw...
Pronouns: *she*,* her*,* hers*

--

*Without ParentsTagger()*
#### ----------------- initialize wild populations ------------------ ####

popA = sim.Population(size=[500, 500, 500],
                            loci=1,
                            subPopNames = ['wild1', 'wild2','wild3'],

infoFields=['fitness','original_sp','broodstock','migrate_to'']) # info
fields for tracking operations

# randomly assign sex
sim.initSex(popA)

# initialize genotypes in each wild population
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[0])
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[1])
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[2])

#### ------------------ evolve wild pops to equilibrium -------------------
####

for gen in range(1,10):
    popA.evolve(
        matingScheme=sim.RandomMating(subPopSize=[500, 500, 500]),
        postOps=[sim.Stat(alleleFreq=0, subPops=[0,1,2],
vars=['alleleFreq','alleleFreq_sp']),
                 sim.Stat(genoFreq=0, subPops=[0,1,2],
vars=['genoFreq','genoFreq_sp']),
                 sim.Stat(popSize=True)],
                 gen = 1)
    print(popA.dvars().subPop[0]['alleleFreq'])

*OUTPUT:*

*{0: defdict({0: 0.537, 1: 0.463})}*
*{0: defdict({0: 0.531, 1: 0.469})}*
*{0: defdict({0: 0.538, 1: 0.462})}*
*{0: defdict({0: 0.53, 1: 0.47})}*
*{0: defdict({0: 0.513, 1: 0.487})}*
*{0: defdict({0: 0.528, 1: 0.472})}*
*{0: defdict({0: 0.525, 1: 0.475})}*
*{0: defdict({0: 0.507, 1: 0.493})}*
*{0: defdict({0: 0.48, 1: 0.52})}*

*With ParentsTagger()*
#### ----------------- initialize wild populations ------------------ ####

popA = sim.Population(size=[500, 500, 500],
                            loci=1,
                            subPopNames = ['wild1', 'wild2','wild3'],

infoFields=['fitness','original_sp','broodstock','migrate_to','father_idx','mother_idx'])
# info fields for tracking operations

# randomly assign sex
sim.initSex(popA)

# initialize genotypes in each wild population
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[0])
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[1])
sim.initGenotype(popA, loci= 0, freq = [0.6, 0.4], subPops=[2])

#### ------------------ evolve wild pops to equilibrium -------------------
####

for gen in range(1,10):
    popA.evolve(
        matingScheme=sim.RandomMating(ops=sim.ParentsTagger(),
                                      subPopSize=[500, 500, 500]),
        postOps=[sim.Stat(alleleFreq=0, subPops=[0,1,2],
vars=['alleleFreq','alleleFreq_sp']),
                 sim.Stat(genoFreq=0, subPops=[0,1,2],
vars=['genoFreq','genoFreq_sp']),
                 sim.Stat(popSize=True)],
                 gen = 1)
    print(popA.dvars().subPop[0]['alleleFreq'])

*OUTPUT:*

*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*
*{0: defdict({0: 1.0})}*

[simuPOP-list] hybridization & errors with splitsubpops on infofield

[Natalie C L. <ncl...@uw...>]

Hi there,

I'm using simupop to model the genetic changes to wild populations of
shellfish associated with shellfish farming. One of the things I'm trying
to do is simulate 'gamete escape', where gametes migrate out of a subpop
and find gametes from another subpop, and the offspring formed settles in
one of the two subpops (essentially hybridization). My plan is to (1) use
an infofield to track the original subpop, (2) merge the subpops, (3) write
a python parent chooser function that ensures the parents come from
different subpops, (4) split the subpop back into it's original subpops,
including the newly formed offspring based on a user defined probability.
First, is there a more straightforward way to achieve this?

Second, I'm still learning the ropes of simupop and having trouble simply
splitting the subpop by an infofield after the original subpops are merged.
Please see my code and error messages below.

Any advice would be greatly appreciated!

Cheers,

*Natalie Lowell*
Graduate Student
School of Aquatic and Fishery Sciences
University of Washington
ncl...@uw...

---

### When I run pop.splitSubPop() with the 'names' argument, I get the
following error, but I only see 4 args...

# initialize population, 3 subpops, 1 locus, and info field for tracking
original subpop through merge / split
pop = sim.Population(size=[100]*3, subPopNames = ['farm','lwild','dwild'],
loci=1, infoFields=['original_sp'])

# set info field to original subpop index
for subPop_idx in range(3):
    for individual in pop.individuals([subPop_idx]):
        individual.original_sp = subPop_idx

# merge subpops
pop.mergeSubPops()

# split subpop into original subpops
pop.splitSubPop(pop = pop, subPop = 0, infoFields = ['original_sp'], names
= ['farm','lwild','dwild'])

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-155-71721699d30c> in <module>()
     14
     15 # split subpop into original subpops
---> 16 pop.splitSubPop(pop = pop, subPop = 0, infoFields =
['original_sp'], names = ['farm','lwild','dwild'])

TypeError: Population_splitSubPop() takes at most 4 arguments (5 given)



### When I run pop.splitSubPop() without the 'names' argument, the error
implies I need the 'sizes' arg,
### but I was under the impression it needs one of three choices: sizes,
proportions, infofields

# initialize population, 3 subpops, 1 locus, and info field for tracking
original subpop through merge / split
pop = sim.Population(size=[100]*3, subPopNames = ['farm','lwild','dwild'],
loci=1, infoFields=['original_sp'])

# set info field to original subpop index
for subPop_idx in range(3):
    for individual in pop.individuals([subPop_idx]):
        individual.original_sp = subPop_idx

# merge subpops
pop.mergeSubPops()

# split subpop into original subpops
pop.splitSubPop(pop = pop, subPop = 0, infoFields = ['original_sp'])

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-157-a5e270e9cf8f> in <module>()
     11
     12 # split subpop into original subpops
---> 13 pop.splitSubPop(pop = pop, subPop = 0, infoFields = ['original_sp'])

TypeError: Required argument 'sizes' (pos 3) not found

[simuPOP-list] (no subject)

[Meije G. <mei...@wa...>]

Dear List,

 

I'm trying to simulate a population of wheat. At each generation I would like to produce a defined number of offsprings per parent. For example parent n°0 produces 2 offsprings, parent n°1 produces 4 offsprings... How is it possible to do this ? In the mating scheme the argument numOffspring is just an integer, while I would need it to be a list with the number of offsprings per parent.

 

Thank you for your help,

 

Meije Gawinowski

 

Re: [simuPOP-list] Tracking birth experience

[John D. <jj...@ud...>]

Ok awesome.

John J. Dougherty III
PhD Student : Bioinformatics & Systems Biology
University of Delaware
(P) (856) 981-9491
jj...@ud...

On Thu, Mar 2, 2017 at 4:25 PM, ITO Tsuyoshi <ito...@ky...>
wrote:

> Thank you for your message.
>
> Bo kindly told me some solutions here.
> https://github.com/BoPeng/simuPOP/issues/34
>
> Thanks to his help, I can now track whether an individual has gave birth
> or not.
>
> Best regards,
> Ito
>
>
> On 2017/03/03 2:10, John Dougherty wrote:
>
>> Hello ITO Tsuyoshi,
>> I have a scheme that I believe will solve your problem but I have been
>> absolutely inundated as of late.
>> If you have not worked out a solution I can probably respond to you at
>> some point later tonight (~8-10 hours).
>> Please let me know if you still have this issue.
>>
>>
>> Sincerely,
>>
>> John J. Dougherty III
>> PhD Student : Bioinformatics & Systems Biology
>> University of Delaware
>> (P) (856) 981-9491
>> jj...@ud... <mailto:jj...@ud...>
>>
>> On Mon, Feb 27, 2017 at 10:36 PM, ITO Tsuyoshi <
>> ito...@ky... <mailto:ito...@ky...>>
>> wrote:
>>
>>     Hello everyone,
>>
>>     I'm trying to simulate a population in overlapping generation, in
>> which females can have offsprings only if they didn't have offsprings in
>> the previous year. Males can have offsprings any time. Although I thought
>> that offspring_idx could be helpful, the index is reset for each mating
>> event. Is there any way to track whether a individual had offsprings in the
>> previous year or not? Any help would be appreciated.
>>
>>     Best regards,
>>     Ito
>>
>>     ------------------------------------------------------------
>> ------------------
>>     Check out the vibrant tech community on one of the world's most
>>     engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>     _______________________________________________
>>     simuPOP-list mailing list
>>     sim...@li... <mailto:sim...@li...u
>> rceforge.net>
>>     https://lists.sourceforge.net/lists/listinfo/simupop-list <
>> https://lists.sourceforge.net/lists/listinfo/simupop-list>
>>
>>
>>

Re: [simuPOP-list] Tracking birth experience

[ITO T. <ito...@ky...>]

Thank you for your message.

Bo kindly told me some solutions here.
https://github.com/BoPeng/simuPOP/issues/34

Thanks to his help, I can now track whether an individual has gave birth or not.

Best regards,
Ito


On 2017/03/03 2:10, John Dougherty wrote:
> Hello ITO Tsuyoshi,
> I have a scheme that I believe will solve your problem but I have been absolutely inundated as of late.
> If you have not worked out a solution I can probably respond to you at some point later tonight (~8-10 hours).
> Please let me know if you still have this issue.
>
>
> Sincerely,
>
> John J. Dougherty III
> PhD Student : Bioinformatics & Systems Biology
> University of Delaware
> (P) (856) 981-9491
> jj...@ud... <mailto:jj...@ud...>
>
> On Mon, Feb 27, 2017 at 10:36 PM, ITO Tsuyoshi <ito...@ky... <mailto:ito...@ky...>> wrote:
>
>     Hello everyone,
>
>     I'm trying to simulate a population in overlapping generation, in which females can have offsprings only if they didn't have offsprings in the previous year. Males can have offsprings any time. Although I thought that offspring_idx could be helpful, the index is reset for each mating event. Is there any way to track whether a individual had offsprings in the previous year or not? Any help would be appreciated.
>
>     Best regards,
>     Ito
>
>     ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>     _______________________________________________
>     simuPOP-list mailing list
>     sim...@li... <mailto:sim...@li...>
>     https://lists.sourceforge.net/lists/listinfo/simupop-list <https://lists.sourceforge.net/lists/listinfo/simupop-list>
>
>

Re: [simuPOP-list] Tracking birth experience

[John D. <jj...@ud...>]

Hello ITO Tsuyoshi,
I have a scheme that I believe will solve your problem but I have been
absolutely inundated as of late.
If you have not worked out a solution I can probably respond to you at some
point later tonight (~8-10 hours).
Please let me know if you still have this issue.


Sincerely,

John J. Dougherty III
PhD Student : Bioinformatics & Systems Biology
University of Delaware
(P) (856) 981-9491
jj...@ud...

On Mon, Feb 27, 2017 at 10:36 PM, ITO Tsuyoshi <
ito...@ky...> wrote:

> Hello everyone,
>
> I'm trying to simulate a population in overlapping generation, in which
> females can have offsprings only if they didn't have offsprings in the
> previous year. Males can have offsprings any time. Although I thought that
> offspring_idx could be helpful, the index is reset for each mating event.
> Is there any way to track whether a individual had offsprings in the
> previous year or not? Any help would be appreciated.
>
> Best regards,
> Ito
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> simuPOP-list mailing list
> sim...@li...
> https://lists.sourceforge.net/lists/listinfo/simupop-list
>

[simuPOP-list] Tracking birth experience

[ITO T. <ito...@ky...>]

Hello everyone,

I'm trying to simulate a population in overlapping generation, in which females can have offsprings only if they didn't have offsprings in the previous year. Males can have offsprings any time. Although I thought that offspring_idx could be helpful, the index is reset for each mating event. Is there any way to track whether a individual had offsprings in the previous year or not? Any help would be appreciated.

Best regards,
Ito

Re: [simuPOP-list] Problem with simuPOP installation

[Bo P. <be...@gm...>]

We are deprecating the mailing list so I just moved your question to
https://github.com/BoPeng/simuPOP/issues/6

On Tue, Oct 18, 2016 at 3:41 PM, Lorenzo Zane <lor...@gm...> wrote:
> Dear all,
> I tried to install simuPOP, after an age that I do not use it.
> I have a win10 system where I just installed python-2.7.12.msi
> (official Python distribution) and python seems to work. I installed
> simuPOP-1.1.7.win-amd64-py2.7.exe on a win10 system and I had no
> warnings.
>
> However when running very simple scripts I have the following message.
>
> Traceback (most recent call last):
>   File "lorenzo.py", line 7, in <module>
>     import simuPOP as sim
>   File "c:\Python27\lib\site-packages\simuPOP\__init__.py", line 323,
> in <module>
>     from simuPOP.simuPOP_std import *
>   File "c:\Python27\lib\site-packages\simuPOP\simuPOP_std.py", line
> 32, in <module>
>     _simuPOP_std = swig_import_helper()
>   File "c:\Python27\lib\site-packages\simuPOP\simuPOP_std.py", line
> 28, in swig_import_helper
>     _mod = imp.load_module('_simuPOP_std', fp, pathname, description)
> ImportError: DLL load failed with error code 14001
>
>
> Any help is appreciated. Thanks a lot and sorry, maybe this is  silly
> question, but I cannot figure out how to fix it.
>
> Lorenzo
>
>
>
>
>
>
> Lorenzo Zane
> Professore Associato di Ecologia
> Presidente del Corso di Studi aggregato di Biologia, Biologia
> Evoluzionistica e Biologia Marina
>
> tel: +39 0498276220
> mobile: +39 3929495233
> skype contact: lolozaup
> https://www.researchgate.net/profile/Lorenzo_Zane
>
> Second Floor- South
> Dipartimento di Biologia
> Università di Padova
> via U. Bassi/58B
> I-35121 Padova
> Italy

[simuPOP-list] Problem with simuPOP installation

[Lorenzo Z. <lor...@gm...>]

Dear all,
I tried to install simuPOP, after an age that I do not use it.
I have a win10 system where I just installed python-2.7.12.msi
(official Python distribution) and python seems to work. I installed
simuPOP-1.1.7.win-amd64-py2.7.exe on a win10 system and I had no
warnings.

However when running very simple scripts I have the following message.

Traceback (most recent call last):
  File "lorenzo.py", line 7, in <module>
    import simuPOP as sim
  File "c:\Python27\lib\site-packages\simuPOP\__init__.py", line 323,
in <module>
    from simuPOP.simuPOP_std import *
  File "c:\Python27\lib\site-packages\simuPOP\simuPOP_std.py", line
32, in <module>
    _simuPOP_std = swig_import_helper()
  File "c:\Python27\lib\site-packages\simuPOP\simuPOP_std.py", line
28, in swig_import_helper
    _mod = imp.load_module('_simuPOP_std', fp, pathname, description)
ImportError: DLL load failed with error code 14001


Any help is appreciated. Thanks a lot and sorry, maybe this is  silly
question, but I cannot figure out how to fix it.

Lorenzo






Lorenzo Zane
Professore Associato di Ecologia
Presidente del Corso di Studi aggregato di Biologia, Biologia
Evoluzionistica e Biologia Marina

tel: +39 0498276220
mobile: +39 3929495233
skype contact: lolozaup
https://www.researchgate.net/profile/Lorenzo_Zane

Second Floor- South
Dipartimento di Biologia
Università di Padova
via U. Bassi/58B
I-35121 Padova
Italy

[simuPOP-list] (no subject)

[Kammonen, J. <juh...@he...>]

unsubscribe

Re: [simuPOP-list] Bug? in the allele frequency

[hmh <hu...@gm...>]

Hi,


It solved it, indeed.


Thanks !



On 29.08.2016 00:25, Bo Peng wrote:
> Hi, Hugo,
>
> I have a quick look at your script and find that your mating scheme 
> uses a PyOperator as ops. This operator set offspring info but does 
> not pass parental genotypes. Please add a MedelianGenoTransmitter or 
> another genotype transmitter before the PyOperator and let me know if 
> this solves your problem.
>
> Cheers,
> Bo
>
> On Sun, Aug 28, 2016 at 11:59 AM, hmh <hu...@gm... 
> <mailto:hu...@gm...>> wrote:
>
>     Hi,
>
>
>     I have a bug in the allele frequency, I don't understand what is
>     wrong in my script, and the bug persist even with the simplest
>     situation '1 locus, 2 alleles, no mutation':
>
>     _Every two generations the allele frequency is set to 0_.
>
>
>     For every generation, the attached script print the allele
>     frequency of the population, and the genotype of the first 5
>     individuals as well as of their 2 parents.
>
>     (Genotypes are 0, 0.5 and 1 where 0.5 means heterozygous)
>
>
>     Probably because of the same bug, their often inconsistency such as:
>
>
>     at the generation N
>
>     Off:1.0 Dad:0.0 Mom:0.0
>
>
>     at the generation N+1
>
>     Off:0.0 Dad:1.0 Mom:1.0
>
>
>     I am using this simupop version :
>
>     # simuPOP Version 1.1.7.1 : Copyright (c) 2004-2016 Bo Peng #
>     Revision 5003 (May 22 2016) for Python 3.5.1+ (64bit, 1thread) #
>     Random Number Generator is set to mt19937 with random seed
>     0x91f07829f57cb62. # This is the standard short allele version
>     with 256 maximum allelic states. # For more information, please
>     visit http://simupop.sourceforge.net, # or email
>     sim...@li...
>     <mailto:sim...@li...> (subscription required).
>
>     Thanks for your help!
>
>     hugo
>
>     -- 
>
>     Hugo Mathé-Hubert
>
>     BU-G19
>
>     postdoc
>
>     eawag (Swiss Federal Institute of Aquatic Science and Technology)
>     Evolutionary Ecology
>     <http://www.eawag.ch/en/department/eco/main-focus/evolutionary-ecology/>-
>     About me
>     <http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/hugo-mathe-hubert/>
>
>     Überlandstrasse 133 P.O.Box 611 8600 Dübendorf, Switzerland
>
>     - - - - - - - - - - - - - - - - - -
>
>     Thoughts appear from doubts and die in convictions. Therefore,
>     doubts are an indication of strength and convictions an indication
>     of weakness. Yet, most people /believe/ the opposite.
>
>     - - - - - - - - - - - - - - - - - -
>
>     Les réflexions naissent dans les doutes et meurent dans les
>     certitudes. Les doutes sont donc un signe de force et les
>     certitudes un signe de faiblesse. La plupart des gens sont
>     pourtant certains du contraire.
>
-- - no title specified

Hugo Mathé-Hubert

BU-G19

postdoc

eawag (Swiss Federal Institute of Aquatic Science and Technology) 
Evolutionary Ecology 
<http://www.eawag.ch/en/department/eco/main-focus/evolutionary-ecology/>- 
About me 
<http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/hugo-mathe-hubert/>

Überlandstrasse 133 P.O.Box 611 8600 Dübendorf, Switzerland

- - - - - - - - - - - - - - - - - -

Thoughts appear from doubts and die in convictions. Therefore, doubts 
are an indication of strength and convictions an indication of weakness. 
Yet, most people believe the opposite.

- - - - - - - - - - - - - - - - - -

Les réflexions naissent dans les doutes et meurent dans les certitudes. 
Les doutes sont donc un signe de force et les certitudes un signe de 
faiblesse. La plupart des gens sont pourtant certains du contraire.

Re: [simuPOP-list] Bug? in the allele frequency

[Bo P. <be...@gm...>]

Hi, Hugo,

I have a quick look at your script and find that your mating scheme uses a
PyOperator as ops. This operator set offspring info but does not pass
parental genotypes. Please add a MedelianGenoTransmitter or another
genotype transmitter before the PyOperator and let me know if this solves
your problem.

Cheers,
Bo

On Sun, Aug 28, 2016 at 11:59 AM, hmh <hu...@gm...> wrote:

> Hi,
>
>
> I have a bug in the allele frequency, I don't understand what is wrong in
> my script, and the bug persist even with the simplest situation '1 locus, 2
> alleles, no mutation':
> *Every two generations the allele frequency is set to 0*.
>
>
> For every generation, the attached script print the allele frequency of
> the population, and the genotype of the first 5 individuals as well as of
> their 2 parents.
>
> (Genotypes are 0, 0.5 and 1 where 0.5 means heterozygous)
>
>
> Probably because of the same bug, their often inconsistency such as:
>
>
> at the generation N
>
> Off:1.0 Dad:0.0 Mom:0.0
>
>
> at the generation N+1
>
> Off:0.0 Dad:1.0 Mom:1.0
>
>
> I am using this simupop version :
>
> # simuPOP Version 1.1.7.1 : Copyright (c) 2004-2016 Bo Peng# Revision 5003 (May 22 2016) for Python 3.5.1+ (64bit, 1thread)# Random Number Generator is set to mt19937 with random seed 0x91f07829f57cb62.# This is the standard short allele version with 256 maximum allelic states.# For more information, please visit http://simupop.sourceforge.net,# or email sim...@li... (subscription required).
>
>
> Thanks for your help!
>
> hugo
>
>
> --
>
> Hugo Mathé-Hubert
>
> BU-G19
>
> postdoc
>
> eawag (Swiss Federal Institute of Aquatic Science and Technology)
> Evolutionary Ecology
> <http://www.eawag.ch/en/department/eco/main-focus/evolutionary-ecology/>
> - About me
> <http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/hugo-mathe-hubert/>
>
>
>
> Überlandstrasse 133
> P.O.Box 611
> 8600 Dübendorf, Switzerland
>
> - - - - - - - - - - - - - - - - - -
>
> Thoughts appear from doubts and die in convictions. Therefore, doubts are
> an indication of strength and convictions an indication of weakness. Yet,
> most people *believe* the opposite.
>
> - - - - - - - - - - - - - - - - - -
>
> Les réflexions naissent dans les doutes et meurent dans les certitudes.
> Les doutes sont donc un signe de force et les certitudes un signe de
> faiblesse. La plupart des gens sont pourtant certains du contraire.
>
>

[simuPOP-list] Bug? in the allele frequency

[hmh <hu...@gm...>]

Hi,


I have a bug in the allele frequency, I don't understand what is wrong 
in my script, and the bug persist even with the simplest situation '1 
locus, 2 alleles, no mutation':

_Every two generations the allele frequency is set to 0_.


For every generation, the attached script print the allele frequency of 
the population, and the genotype of the first 5 individuals as well as 
of their 2 parents.

(Genotypes are 0, 0.5 and 1 where 0.5 means heterozygous)


Probably because of the same bug, their often inconsistency such as:


at the generation N

Off:1.0 Dad:0.0 Mom:0.0


at the generation N+1

Off:0.0 Dad:1.0 Mom:1.0


I am using this simupop version :

# simuPOP Version 1.1.7.1 : Copyright (c) 2004-2016 Bo Peng # Revision 
5003 (May 22 2016) for Python 3.5.1+ (64bit, 1thread) # Random Number 
Generator is set to mt19937 with random seed 0x91f07829f57cb62. # This 
is the standard short allele version with 256 maximum allelic states. # 
For more information, please visit http://simupop.sourceforge.net, # or 
email sim...@li... (subscription required).


Thanks for your help!

hugo


-- 
Bug? in the allele frequency

Hugo Mathé-Hubert

BU-G19

postdoc

eawag (Swiss Federal Institute of Aquatic Science and Technology)
Evolutionary Ecology 
<http://www.eawag.ch/en/department/eco/main-focus/evolutionary-ecology/>- 
About me 
<http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/hugo-mathe-hubert/>

Überlandstrasse 133
P.O.Box 611
8600 Dübendorf, Switzerland

- - - - - - - - - - - - - - - - - -

Thoughts appear from doubts and die in convictions. Therefore, doubts 
are an indication of strength and convictions an indication of weakness. 
Yet, most people /believe/ the opposite.

- - - - - - - - - - - - - - - - - -

Les réflexions naissent dans les doutes et meurent dans les certitudes. 
Les doutes sont donc un signe de force et les certitudes un signe de 
faiblesse. La plupart des gens sont pourtant certains du contraire.

[simuPOP-list] Bug? in the allele frequency

[hmh <hu...@gm...>]

Hi,


I have a bug in the allele frequency, I don't understand what is wrong 
in my script, and the bug persist even with the simplest situation '1 
locus, 2 alleles, no mutation'

_The bug is that every two generations the allele frequency is set to 0_.


For every generation, the attached script print the allele frequency of 
the population, and the genotype of the first 5 individuals as well as 
of their 2 parents.

(Genotypes are 0, 0.5 and 1 where 0.5 means heterozygous)


Probably because of the same bug, there are often inconsistency such as:


at the generation N

Off:1.0 Dad:0.0 Mom:0.0


at the generation N+1

Off:0.0 Dad:1.0 Mom:1.0


I am using this simupop version :

# simuPOP Version 1.1.7.1 : Copyright (c) 2004-2016 Bo Peng # Revision 
5003 (May 22 2016) for Python 3.5.1+ (64bit, 1thread) # Random Number 
Generator is set to mt19937 with random seed 0x91f07829f57cb62. # This 
is the standard short allele version with 256 maximum allelic states. # 
For more information, please visit http://simupop.sourceforge.net, # or 
email sim...@li... (subscription required).


Thanks for your help!

hugo


-- 
- no title specified

Hugo Mathé-Hubert

BU-G19

postdoc

eawag (Swiss Federal Institute of Aquatic Science and Technology)
Evolutionary Ecology 
<http://www.eawag.ch/en/department/eco/main-focus/evolutionary-ecology/>- 
About me 
<http://www.eawag.ch/en/aboutus/portrait/organisation/staff/profile/hugo-mathe-hubert/>

Überlandstrasse 133
P.O.Box 611
8600 Dübendorf, Switzerland

- - - - - - - - - - - - - - - - - -

Thoughts appear from doubts and die in convictions. Therefore, doubts 
are an indication of strength and convictions an indication of weakness. 
Yet, most people /believe/ the opposite.

- - - - - - - - - - - - - - - - - -

Les réflexions naissent dans les doutes et meurent dans les certitudes. 
Les doutes sont donc un signe de force et les certitudes un signe de 
faiblesse. La plupart des gens sont pourtant certains du contraire.

Re: [simuPOP-list] Examples of argparse instead of simuOpt.Params()

[Peng,Bo <bp...@md...>]

Hi, Zhian,

We are moving to github so please start a ticket at
github.com/BoPeng/simuPOP/issues for new topics.

Yes, simuOpt.Params() was developed before argparse was available.
Although it still has some unique features (notably validation,
configuration file, and GUI), it is not as powerful and robust as argparse
as a general-purpose argument parser. I have switched to argparse and
found it quite nice to use in general.

For your question, argparse does not have built in support for
configuration files. I usually use json or yaml for such features and
http://codereview.stackexchange.com/questions/110108/using-argparse-with-pa
rameters-defined-in-config-file provides an example. Basically, I would
give default values to all command line options in argparse and an option
(e.g. -c ) to read a configuration file. The values read from
configuration file (e.g. cfg = yaml.safe_load(config)) would then be used
to populate the arguments. Saving parameters to a configuration file is
also easy (e.g. yaml.safe_dump()) if you do not have high requirement for
readability of configuration file.

Hope this helps,
Bo

On 8/19/16, 11:57 AM, "Zhian Kamvar" <ka...@sc...>
wrote:

>Hello,
>
>I was wondering if anyone has an example of using argparse instead of
>simuOpt.Params() given that the latter is now deprecated [0]? I'm looking
>for an example that encapsulates reading in arguments from the command
>line OR a configuration file and then writing them to a configuration
>file. 
>
>I've found a blog post [1] on advanced argument parsing and will be
>attempting to refactor my script. If I come up with a solution before
>anyone answers, I'll answer my own question.
>
>Thanks,
>Zhian
>
>[0]: 
>http://simupop.sourceforge.net/manual_svn/build/userGuide_ch7_sec1.html
>[1]: 
>http://tricksntweaks.blogspot.com/2013/05/advance-argument-parsing-in-pyth
>on.html
>--------------------------------------------------------------------------
>----
>_______________________________________________
>simuPOP-list mailing list
>sim...@li...
>https://lists.sourceforge.net/lists/listinfo/simupop-list

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[simuPOP-list] Examples of argparse instead of simuOpt.Params()

[Zhian K. <ka...@sc...>]

Hello,

I was wondering if anyone has an example of using argparse instead of simuOpt.Params() given that the latter is now deprecated [0]? I'm looking for an example that encapsulates reading in arguments from the command line OR a configuration file and then writing them to a configuration file. 

I've found a blog post [1] on advanced argument parsing and will be attempting to refactor my script. If I come up with a solution before anyone answers, I'll answer my own question.

Thanks,
Zhian

[0]: http://simupop.sourceforge.net/manual_svn/build/userGuide_ch7_sec1.html
[1]: http://tricksntweaks.blogspot.com/2013/05/advance-argument-parsing-in-python.html

Re: [simuPOP-list] RandomParentChooser in HomoMating

[Zhian K. <ka...@sc...>]

But, from the output of the code you posted, it shows an even distribution of sex in the offspring, but the individual IDs only match the mother ID. Is this a bug?

>>> print([x.sex() for x in pop.individuals()])
[2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 1, 2, 2, 2, 1, 2, 2, 1, 2, 2, 1, 2, 2, 1, 1, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 2, 2, 1, 2, 2, 1, 1, 2, 1, 2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 2, 1, 1, 1, 2, 1]
>>> print(pop.indInfo('mother_id'))
(26.0, 89.0, 24.0, 87.0, 62.0, 80.0, 29.0, 72.0, 43.0, 89.0, 2.0, 67.0, 10.0, 16.0, 85.0, 84.0, 46.0, 83.0, 6.0, 80.0, 7.0, 15.0, 77.0, 36.0, 46.0, 4.0, 19.0, 52.0, 100.0, 15.0, 53.0, 11.0, 41.0, 46.0, 14.0, 6.0, 9.0, 59.0, 88.0, 70.0, 17.0, 36.0, 67.0, 44.0, 87.0, 83.0, 100.0, 86.0, 90.0, 84.0, 86.0, 4.0, 55.0, 67.0, 77.0, 73.0, 58.0, 70.0, 10.0, 52.0, 38.0, 56.0, 1.0, 78.0, 42.0, 28.0, 52.0, 14.0, 28.0, 77.0, 91.0, 100.0, 47.0, 80.0, 96.0, 22.0, 38.0, 22.0, 17.0, 92.0, 90.0, 86.0, 88.0, 71.0, 61.0, 6.0, 91.0, 1.0, 58.0, 35.0, 77.0, 95.0, 18.0, 52.0, 14.0, 70.0, 82.0, 29.0, 65.0, 5.0)
>>> print(pop.indInfo('father_id'))
(0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
>>> print(pop.indInfo('ind_id'))
(26.0, 89.0, 24.0, 87.0, 62.0, 80.0, 29.0, 72.0, 43.0, 89.0, 2.0, 67.0, 10.0, 16.0, 85.0, 84.0, 46.0, 83.0, 6.0, 80.0, 7.0, 15.0, 77.0, 36.0, 46.0, 4.0, 19.0, 52.0, 100.0, 15.0, 53.0, 11.0, 41.0, 46.0, 14.0, 6.0, 9.0, 59.0, 88.0, 70.0, 17.0, 36.0, 67.0, 44.0, 87.0, 83.0, 100.0, 86.0, 90.0, 84.0, 86.0, 4.0, 55.0, 67.0, 77.0, 73.0, 58.0, 70.0, 10.0, 52.0, 38.0, 56.0, 1.0, 78.0, 42.0, 28.0, 52.0, 14.0, 28.0, 77.0, 91.0, 100.0, 47.0, 80.0, 96.0, 22.0, 38.0, 22.0, 17.0, 92.0, 90.0, 86.0, 88.0, 71.0, 61.0, 6.0, 91.0, 1.0, 58.0, 35.0, 77.0, 95.0, 18.0, 52.0, 14.0, 70.0, 82.0, 29.0, 65.0, 5.0)

Zhian

For posterity, here's the info of the simuPOP build I have:

Python 3.4.4 |Anaconda custom (x86_64)| (default, Jan  9 2016, 17:30:09)
[GCC 4.2.1 (Apple Inc. build 5577)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import simuPOP as sim
simuPOP Version 1.1.7 : Copyright (c) 2004-2016 Bo Peng
Revision 5000 (Jan 21 2016) for Python 3.4.4 (64bit, 0thread)
Random Number Generator is set to mt19937 with random seed 0xe684ed2f1dd65325.
This is the standard short allele version with 256 maximum allelic states.
For more information, please visit http://simupop.sourceforge.net,
or email sim...@li... (subscription required).


> On Jun 30, 2016, at 20:44 , Bo Peng <be...@gm...> wrote:
> 
> ​Males and females have equal probability to be chosen and propagate here. If you notice one sex prevails, it must be a random process (similar to genetic drift) that causes one sex reaches fixation.
> 
> Bo
> ​
> 
> On Thu, Jun 30, 2016 at 10:35 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
> Yes, I did initialize the sex. In this example, while there is an equal distribution of sex ratios, they appear to be propagated through the maternal parent, which means that the sex of the offspring does not match the sex of the parent. Is there a way for the males to also create clones and to keep the sex of the parent?
> 
> Zhian
> 
>> On Jun 30, 2016, at 20:16 , Bo Peng <be...@gm... <mailto:be...@gm...>> wrote:
>> 
>> Did you initialize sex of parents? I see different sex of offspring from the following code:
>> 
>> import simuPOP as sim
>> 
>> pop = sim.Population(100, infoFields=['ind_id', 'father_id', 'mother_id'])
>> 
>> pop.evolve(
>>     initOps = [sim.IdTagger(), sim.InitSex()],
>>     matingScheme=sim.HomoMating(
>>         chooser = sim.RandomParentChooser(),
>>         generator = sim.OffspringGenerator(
>>             ops = [
>>                 sim.CloneGenoTransmitter(),
>>                 sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>>                 ],
>>             numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 1)
>>             )
>>     ),
>>     #postOps = [
>>     gen = 1
>>     
>> )
>> print([x.sex() for x in pop.individuals()])
>> print(pop.indInfo('mother_id'))
>> print(pop.indInfo('father_id'))
>> 
>> Bo
>> 
>> On Thu, Jun 30, 2016 at 10:13 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
>> If it selects a single individual randomly, then that individual should be copied to the next generation through CloneGenoTransmitter(), and you would have roughly the same ratio of males to females in the next generation, but in this case, I'm only seeing maternal genotypes. Is there something I'm missing in my function that's causing only one sex to be passed through to the next generation?
>> 
>> Zhian
>> 
>>> On Jun 30, 2016, at 20:06 , Bo Peng <be...@gm... <mailto:be...@gm...>> wrote:
>>> 
>>> Yes. RandomParentChooser will choose one parent (another being NULL) regardless of sex (http://simupop.sourceforge.net/manual_svn/build/refManual_ch2_sec3.html#class-randomparentchooser <http://simupop.sourceforge.net/manual_svn/build/refManual_ch2_sec3.html#class-randomparentchooser>).
>>> 
>>> Bo
>>> 
>>> 
>>> On Thu, Jun 30, 2016 at 10:01 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
>>> Hi Bo,
>>> 
>>> I realize I left a few details out:
>>> 
>>> The population I'm trying to simulate is an Oomycete population, where either "sex" (in reality mating types) can produce clonal offspring. In this situation, only one mating type is producing offspring. 
>>> 
>>> In the documentation of the CloneGenoTransmitter(), it states that if two parents are supplied, the maternal genotype will be copied. Since I want a mixture of both male and female clones, I tried to use RandomParentChooser(), which I assume randomly selects a single individual. Am I wrong thinking that RandomParentChooser() selects a single individual?
>>> 
>>> Thanks,
>>> Zhian
>>> 
>>> 
>>>> On Jun 30, 2016, at 18:34 , Bo Peng <be...@gm... <mailto:be...@gm...>> wrote:
>>>> 
>>>> Hi, Zhian,
>>>> 
>>>> I am not sure what is the problem here because your mating scheme works as expected when I run a test simulation. When I set numOffspring=1, the mother_id and father_id of the population are
>>>> 
>>>> (90.0, 7.0, 79.0, 14.0, 68.0, 24.0, 79.0, 80.0, 60.0, 71.0, 100.0, 28.0, 97.0, 13.0, 64.0, 85.0, 43.0, 98.0, 59.0, 46.0, 2.0, 42.0, 46.0, 15.0, 79.0, 38.0, 16.0, 32.0, 75.0, 61.0, 4.0, 71.0, 7.0, 71.0, 84.0, 94.0, 16.0, 62.0, 31.0, 24.0, 36.0, 83.0, 75.0, 10.0, 27.0, 27.0, 6.0, 42.0, 41.0, 74.0, 31.0, 12.0, 16.0, 22.0, 58.0, 25.0, 43.0, 15.0, 12.0, 3.0, 52.0, 64.0, 81.0, 22.0, 5.0, 18.0, 51.0, 47.0, 57.0, 33.0, 19.0, 4.0, 41.0, 60.0, 55.0, 9.0, 71.0, 19.0, 18.0, 91.0, 62.0, 18.0, 64.0, 44.0, 78.0, 49.0, 49.0, 83.0, 49.0, 53.0, 93.0, 97.0, 82.0, 8.0, 9.0, 12.0, 99.0, 99.0, 39.0, 95.0)
>>>> 
>>>> (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
>>>> 
>>>> So only mothers are chosen. If you have numOffspring as specified, several consecutive offspring will share a mother.
>>>> 
>>>> Cheers,
>>>> 
>>>> Bo
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Thu, Jun 30, 2016 at 6:09 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
>>>> Hello,
>>>> 
>>>> I'm wondering if I can construct a scenario of diploid clonal reproduction by utilizing RandomParentChooser in HomoMating:
>>>> 
>>>> 
>>>> sim.HomoMating(
>>>>     chooser = sim.RandomParentChooser(),
>>>>     generator = sim.OffspringGenerator(
>>>>         ops = [
>>>>             sim.CloneGenoTransmitter(),
>>>>             sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>>>>             ],
>>>>         numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 3)
>>>>         )
>>>>     )
>>>> 
>>>> I expect that the chooser would select a single parent, but when I run the simulation, it appears that two parents are chosen since I only have females left in the population ( as documented in the CloneGenoTransmitter ). Is there a way to address this?
>>>> 
>>>> Thanks,
>>>> Zhian
>>>> ------------------------------------------------------------------------------
>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>>>> present their vision of the future. This family event has something for
>>>> everyone, including kids. Get more information and register today.
>>>> http://sdm.link/attshape <http://sdm.link/attshape>
>>>> _______________________________________________
>>>> simuPOP-list mailing list
>>>> sim...@li... <mailto:sim...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/simupop-list <https://lists.sourceforge.net/lists/listinfo/simupop-list>
>>>> 
>>> 
>>> 
>> 
>> 
> 
> 

Re: [simuPOP-list] RandomParentChooser in HomoMating

[Bo P. <be...@gm...>]

​Males and females have equal probability to be chosen and propagate here.
If you notice one sex prevails, it must be a random process (similar to
genetic drift) that causes one sex reaches fixation.

Bo
​

On Thu, Jun 30, 2016 at 10:35 PM, Zhian Kamvar <
ka...@sc...> wrote:

> Yes, I did initialize the sex. In this example, while there is an equal
> distribution of sex ratios, they appear to be propagated through the
> maternal parent, which means that the sex of the offspring does not match
> the sex of the parent. Is there a way for the males to also create clones
> and to keep the sex of the parent?
>
> Zhian
>
> On Jun 30, 2016, at 20:16 , Bo Peng <be...@gm...> wrote:
>
> Did you initialize sex of parents? I see different sex of offspring from
> the following code:
>
> import simuPOP as sim
>
> pop = sim.Population(100, infoFields=['ind_id', 'father_id', 'mother_id'])
>
> pop.evolve(
>     initOps = [sim.IdTagger(), sim.InitSex()],
>     matingScheme=sim.HomoMating(
>         chooser = sim.RandomParentChooser(),
>         generator = sim.OffspringGenerator(
>             ops = [
>                 sim.CloneGenoTransmitter(),
>                 sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>                 ],
>             numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 1)
>             )
>     ),
>     #postOps = [
>     gen = 1
>
> )
> print([x.sex() for x in pop.individuals()])
> print(pop.indInfo('mother_id'))
> print(pop.indInfo('father_id'))
>
> Bo
>
> On Thu, Jun 30, 2016 at 10:13 PM, Zhian Kamvar <
> ka...@sc...> wrote:
>
>> If it selects a single individual randomly, then that individual should
>> be copied to the next generation through CloneGenoTransmitter(), and you
>> would have roughly the same ratio of males to females in the next
>> generation, but in this case, I'm only seeing maternal genotypes. Is there
>> something I'm missing in my function that's causing only one sex to be
>> passed through to the next generation?
>>
>> Zhian
>>
>> On Jun 30, 2016, at 20:06 , Bo Peng <be...@gm...> wrote:
>>
>> Yes. RandomParentChooser will choose one parent (another being NULL)
>> regardless of sex (
>> http://simupop.sourceforge.net/manual_svn/build/refManual_ch2_sec3.html#class-randomparentchooser
>> ).
>>
>> Bo
>>
>>
>> On Thu, Jun 30, 2016 at 10:01 PM, Zhian Kamvar <
>> ka...@sc...> wrote:
>>
>>> Hi Bo,
>>>
>>> I realize I left a few details out:
>>>
>>> The population I'm trying to simulate is an Oomycete population, where
>>> either "sex" (in reality mating types) can produce clonal offspring. In
>>> this situation, only one mating type is producing offspring.
>>>
>>> In the documentation of the CloneGenoTransmitter(), it states that if
>>> two parents are supplied, the maternal genotype will be copied. Since I
>>> want a mixture of both male and female clones, I tried to use
>>> RandomParentChooser(), which I assume randomly selects a single individual.
>>> Am I wrong thinking that RandomParentChooser() selects a single individual?
>>>
>>> Thanks,
>>> Zhian
>>>
>>>
>>> On Jun 30, 2016, at 18:34 , Bo Peng <be...@gm...> wrote:
>>>
>>> Hi, Zhian,
>>>
>>> I am not sure what is the problem here because your mating scheme works
>>> as expected when I run a test simulation. When I set numOffspring=1, the
>>> mother_id and father_id of the population are
>>>
>>> (90.0, 7.0, 79.0, 14.0, 68.0, 24.0, 79.0, 80.0, 60.0, 71.0, 100.0, 28.0,
>>> 97.0, 13.0, 64.0, 85.0, 43.0, 98.0, 59.0, 46.0, 2.0, 42.0, 46.0, 15.0,
>>> 79.0, 38.0, 16.0, 32.0, 75.0, 61.0, 4.0, 71.0, 7.0, 71.0, 84.0, 94.0, 16.0,
>>> 62.0, 31.0, 24.0, 36.0, 83.0, 75.0, 10.0, 27.0, 27.0, 6.0, 42.0, 41.0,
>>> 74.0, 31.0, 12.0, 16.0, 22.0, 58.0, 25.0, 43.0, 15.0, 12.0, 3.0, 52.0,
>>> 64.0, 81.0, 22.0, 5.0, 18.0, 51.0, 47.0, 57.0, 33.0, 19.0, 4.0, 41.0, 60.0,
>>> 55.0, 9.0, 71.0, 19.0, 18.0, 91.0, 62.0, 18.0, 64.0, 44.0, 78.0, 49.0,
>>> 49.0, 83.0, 49.0, 53.0, 93.0, 97.0, 82.0, 8.0, 9.0, 12.0, 99.0, 99.0, 39.0,
>>> 95.0)
>>>
>>> (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
>>> 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
>>>
>>> So only mothers are chosen. If you have numOffspring as specified,
>>> several consecutive offspring will share a mother.
>>>
>>> Cheers,
>>>
>>> Bo
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Jun 30, 2016 at 6:09 PM, Zhian Kamvar <
>>> ka...@sc...> wrote:
>>>
>>>> Hello,
>>>>
>>>> I'm wondering if I can construct a scenario of diploid clonal
>>>> reproduction by utilizing RandomParentChooser in HomoMating:
>>>>
>>>>
>>>> sim.HomoMating(
>>>>     chooser = sim.RandomParentChooser(),
>>>>     generator = sim.OffspringGenerator(
>>>>         ops = [
>>>>             sim.CloneGenoTransmitter(),
>>>>             sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>>>>             ],
>>>>         numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 3)
>>>>         )
>>>>     )
>>>>
>>>> I expect that the chooser would select a single parent, but when I run
>>>> the simulation, it appears that two parents are chosen since I only have
>>>> females left in the population ( as documented in the CloneGenoTransmitter
>>>> ). Is there a way to address this?
>>>>
>>>> Thanks,
>>>> Zhian
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>>>> present their vision of the future. This family event has something for
>>>> everyone, including kids. Get more information and register today.
>>>> http://sdm.link/attshape
>>>> _______________________________________________
>>>> simuPOP-list mailing list
>>>> sim...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/simupop-list
>>>>
>>>
>>>
>>>
>>
>>
>
>

Re: [simuPOP-list] RandomParentChooser in HomoMating

[Zhian K. <ka...@sc...>]

Yes, I did initialize the sex. In this example, while there is an equal distribution of sex ratios, they appear to be propagated through the maternal parent, which means that the sex of the offspring does not match the sex of the parent. Is there a way for the males to also create clones and to keep the sex of the parent?

Zhian

> On Jun 30, 2016, at 20:16 , Bo Peng <be...@gm...> wrote:
> 
> Did you initialize sex of parents? I see different sex of offspring from the following code:
> 
> import simuPOP as sim
> 
> pop = sim.Population(100, infoFields=['ind_id', 'father_id', 'mother_id'])
> 
> pop.evolve(
>     initOps = [sim.IdTagger(), sim.InitSex()],
>     matingScheme=sim.HomoMating(
>         chooser = sim.RandomParentChooser(),
>         generator = sim.OffspringGenerator(
>             ops = [
>                 sim.CloneGenoTransmitter(),
>                 sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>                 ],
>             numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 1)
>             )
>     ),
>     #postOps = [
>     gen = 1
>     
> )
> print([x.sex() for x in pop.individuals()])
> print(pop.indInfo('mother_id'))
> print(pop.indInfo('father_id'))
> 
> Bo
> 
> On Thu, Jun 30, 2016 at 10:13 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
> If it selects a single individual randomly, then that individual should be copied to the next generation through CloneGenoTransmitter(), and you would have roughly the same ratio of males to females in the next generation, but in this case, I'm only seeing maternal genotypes. Is there something I'm missing in my function that's causing only one sex to be passed through to the next generation?
> 
> Zhian
> 
>> On Jun 30, 2016, at 20:06 , Bo Peng <be...@gm... <mailto:be...@gm...>> wrote:
>> 
>> Yes. RandomParentChooser will choose one parent (another being NULL) regardless of sex (http://simupop.sourceforge.net/manual_svn/build/refManual_ch2_sec3.html#class-randomparentchooser <http://simupop.sourceforge.net/manual_svn/build/refManual_ch2_sec3.html#class-randomparentchooser>).
>> 
>> Bo
>> 
>> 
>> On Thu, Jun 30, 2016 at 10:01 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
>> Hi Bo,
>> 
>> I realize I left a few details out:
>> 
>> The population I'm trying to simulate is an Oomycete population, where either "sex" (in reality mating types) can produce clonal offspring. In this situation, only one mating type is producing offspring. 
>> 
>> In the documentation of the CloneGenoTransmitter(), it states that if two parents are supplied, the maternal genotype will be copied. Since I want a mixture of both male and female clones, I tried to use RandomParentChooser(), which I assume randomly selects a single individual. Am I wrong thinking that RandomParentChooser() selects a single individual?
>> 
>> Thanks,
>> Zhian
>> 
>> 
>>> On Jun 30, 2016, at 18:34 , Bo Peng <be...@gm... <mailto:be...@gm...>> wrote:
>>> 
>>> Hi, Zhian,
>>> 
>>> I am not sure what is the problem here because your mating scheme works as expected when I run a test simulation. When I set numOffspring=1, the mother_id and father_id of the population are
>>> 
>>> (90.0, 7.0, 79.0, 14.0, 68.0, 24.0, 79.0, 80.0, 60.0, 71.0, 100.0, 28.0, 97.0, 13.0, 64.0, 85.0, 43.0, 98.0, 59.0, 46.0, 2.0, 42.0, 46.0, 15.0, 79.0, 38.0, 16.0, 32.0, 75.0, 61.0, 4.0, 71.0, 7.0, 71.0, 84.0, 94.0, 16.0, 62.0, 31.0, 24.0, 36.0, 83.0, 75.0, 10.0, 27.0, 27.0, 6.0, 42.0, 41.0, 74.0, 31.0, 12.0, 16.0, 22.0, 58.0, 25.0, 43.0, 15.0, 12.0, 3.0, 52.0, 64.0, 81.0, 22.0, 5.0, 18.0, 51.0, 47.0, 57.0, 33.0, 19.0, 4.0, 41.0, 60.0, 55.0, 9.0, 71.0, 19.0, 18.0, 91.0, 62.0, 18.0, 64.0, 44.0, 78.0, 49.0, 49.0, 83.0, 49.0, 53.0, 93.0, 97.0, 82.0, 8.0, 9.0, 12.0, 99.0, 99.0, 39.0, 95.0)
>>> 
>>> (0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
>>> 
>>> So only mothers are chosen. If you have numOffspring as specified, several consecutive offspring will share a mother.
>>> 
>>> Cheers,
>>> 
>>> Bo
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Thu, Jun 30, 2016 at 6:09 PM, Zhian Kamvar <ka...@sc... <mailto:ka...@sc...>> wrote:
>>> Hello,
>>> 
>>> I'm wondering if I can construct a scenario of diploid clonal reproduction by utilizing RandomParentChooser in HomoMating:
>>> 
>>> 
>>> sim.HomoMating(
>>>     chooser = sim.RandomParentChooser(),
>>>     generator = sim.OffspringGenerator(
>>>         ops = [
>>>             sim.CloneGenoTransmitter(),
>>>             sim.PedigreeTagger(infoFields=['mother_id', 'father_id']),
>>>             ],
>>>         numOffspring=(sim.UNIFORM_DISTRIBUTION, 1, 3)
>>>         )
>>>     )
>>> 
>>> I expect that the chooser would select a single parent, but when I run the simulation, it appears that two parents are chosen since I only have females left in the population ( as documented in the CloneGenoTransmitter ). Is there a way to address this?
>>> 
>>> Thanks,
>>> Zhian
>>> ------------------------------------------------------------------------------
>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>>> present their vision of the future. This family event has something for
>>> everyone, including kids. Get more information and register today.
>>> http://sdm.link/attshape <http://sdm.link/attshape>
>>> _______________________________________________
>>> simuPOP-list mailing list
>>> sim...@li... <mailto:sim...@li...>
>>> https://lists.sourceforge.net/lists/listinfo/simupop-list <https://lists.sourceforge.net/lists/listinfo/simupop-list>
>>> 
>> 
>> 
> 
>