Error loading frecuencies from datafile

[Andrés Pérez-Figueroa]

When setting to read frecuencies from datafile it launchs this error:

Traceback (most recent call last):
  File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in __simulate
    genome = Genome(pars)
  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12, in __init__
    self.createOps()
  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 58, in createOps
    self._loadData(self.filename)
AttributeError: Genome instance has no attribute '_loadData'

[Andrés Pérez-Figueroa (andres-perez-figueroa)]

This is solved easily by renaming method from loadData to _loadData or vice-versa. I didn't commited it because there is a matrix called frecs that used to be a numpy matrix and I prefer you choose a new way to set this.

[Tiago Antao (tiagoantao)]

Don't forget to push the change so that I can see it (bzr push)

You will probably need to set up an ssh key with launchpad

[Tiago Antao (tiagoantao)]

Ok, misunderstood your comment sorry, I will fix it.

[Tiago Antao (tiagoantao)]

Can you please send me an example data file? Maybe in private is the data is sensitive...

[Andrés Pérez-Figueroa (andres-perez-figueroa)]

this is a dataset for frequencies of 48 microsats used for all examples.

[Andrés Pérez-Figueroa (andres-perez-figueroa)]

push or commit?

I've tried

bzr commit -m "Fixed Bug: 598460" src/NewAge/Sim/LifeHistory.py

but it causes:
bzr: ERROR: Cannot lock
LockDir(lp-69743952:///~tiagoantao/newage/trunk/.bzr/branchlock): Transport
operation not possible: readonly transport

I've already have a ssh-key in launchpad. Maybe you have to give me write
access....

2010/6/25 Tiago Antao <email address hidden>

> Don't forget to push the change so that I can see it (bzr push)
>
> You will probably need to set up an ssh key with launchpad
>
> --
> Error loading frecuencies from datafile
> https://bugs.launchpad.net/bugs/598312
> You received this bug notification because you are a direct subscriber
> of the bug.
>
> Status in newAge: A population genetics workbench to simulate and analise
> age-structured populations: New
>
> Bug description:
> When setting to read frecuencies from datafile it launchs this error:
>
> Traceback (most recent call last):
> File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in
> __simulate
> genome = Genome(pars)
> File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12,
> in __init__
> self.createOps()
> File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 58,
> in createOps
> self._loadData(self.filename)
> AttributeError: Genome instance has no attribute '_loadData'
>
> To unsubscribe from this bug, go to:
> https://bugs.launchpad.net/newage/+bug/598312/+subscribe
>

--
**********************************************
Andrés Pérez-Figueroa.

Postdoc at

Dep. Bioquímica, Xenética e Inmunoloxía.
Facultade de Bioloxía. Universidade de Vigo.
36310 Vigo. Spain.
-------------------------------------------------------
web: http://webs.uvigo.es/anpefi
e-mail: <email address hidden>
Tfn/fax: [phone]
Skype: andres.perez.figueroa
**********************************************

[Tiago Antao (tiagoantao)]

Don't worry, I will sort this one myself.
I misunderstood your previous comment and thought you tried to commit.
The current version is probably inconsistent with your repository as I
have made some changes (corrected most of the bugs by now).

Tiago

2010/6/25 Andrés Pérez-Figueroa <email address hidden>:
> push or commit?
>
> I've tried
>
> bzr commit -m "Fixed Bug: 598460" src/NewAge/Sim/LifeHistory.py
>
>
> but  it causes:
> bzr: ERROR: Cannot lock
> LockDir(lp-69743952:///~tiagoantao/newage/trunk/.bzr/branchlock): Transport
> operation not possible: readonly transport
>
> I've already have a ssh-key in launchpad. Maybe you have to give me write
> access....
>
> 2010/6/25 Tiago Antao <email address hidden>
>
>> Don't forget to push the change so that I can see it (bzr push)
>>
>> You will probably need to set up an ssh key with launchpad
>>
>> --
>> Error loading frecuencies from datafile
>> https://bugs.launchpad.net/bugs/598312
>> You received this bug notification because you are a direct subscriber
>> of the bug.
>>
>> Status in newAge: A population genetics workbench to simulate and analise
>> age-structured populations: New
>>
>> Bug description:
>> When setting to read frecuencies from datafile it launchs this error:
>>
>> Traceback (most recent call last):
>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in
>> __simulate
>>    genome = Genome(pars)
>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12,
>> in __init__
>>    self.createOps()
>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 58,
>> in createOps
>>    self._loadData(self.filename)
>> AttributeError: Genome instance has no attribute '_loadData'
>>
>> To unsubscribe from this bug, go to:
>> https://bugs.launchpad.net/newage/+bug/598312/+subscribe
>>
>
>
> --
> **********************************************
> Andrés Pérez-Figueroa.
>
> Postdoc at
>
> Dep. Bioquímica, Xenética e Inmunoloxía.
> Facultade de Bioloxía. Universidade de Vigo.
> 36310 Vigo. Spain.
> -------------------------------------------------------
> web: http://webs.uvigo.es/anpefi
> e-mail: <email address hidden>
> Tfn/fax: [phone]
> Skype: andres.perez.figueroa
> **********************************************
>
> --
> Error loading frecuencies from datafile
> https://bugs.launchpad.net/bugs/598312
> You received this bug notification because you are a member of newAge,
> which is the registrant for newAge.
>
> Status in newAge: A population genetics workbench to simulate and analise age-structured populations: New
>
> Bug description:
> When setting to read frecuencies from datafile it launchs this error:
>
> Traceback (most recent call last):
>  File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in __simulate
>    genome = Genome(pars)
>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12, in __init__
>    self.createOps()
>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 58, in createOps
>    self._loadData(self.filename)
> AttributeError: Genome instance has no attribute '_loadData'
>
>
>

--
"If you want to get laid, go to college. If you want an educ...

[Tiago Antao (tiagoantao)]

As it stands, the code only allows the load of microsatellite data,
not SNPS, correct?

2010/6/25 Tiago Antão <email address hidden>:
> Don't worry, I will sort this one myself.
> I misunderstood your previous comment and thought you tried to commit.
> The current version is probably inconsistent with your repository as I
> have made some changes (corrected most of the bugs by now).
>
> Tiago
>
> 2010/6/25 Andrés Pérez-Figueroa <email address hidden>:
>> push or commit?
>>
>> I've tried
>>
>> bzr commit -m "Fixed Bug: 598460" src/NewAge/Sim/LifeHistory.py
>>
>>
>> but  it causes:
>> bzr: ERROR: Cannot lock
>> LockDir(lp-69743952:///~tiagoantao/newage/trunk/.bzr/branchlock): Transport
>> operation not possible: readonly transport
>>
>> I've already have a ssh-key in launchpad. Maybe you have to give me write
>> access....
>>
>> 2010/6/25 Tiago Antao <email address hidden>
>>
>>> Don't forget to push the change so that I can see it (bzr push)
>>>
>>> You will probably need to set up an ssh key with launchpad
>>>
>>> --
>>> Error loading frecuencies from datafile
>>> https://bugs.launchpad.net/bugs/598312
>>> You received this bug notification because you are a direct subscriber
>>> of the bug.
>>>
>>> Status in newAge: A population genetics workbench to simulate and analise
>>> age-structured populations: New
>>>
>>> Bug description:
>>> When setting to read frecuencies from datafile it launchs this error:
>>>
>>> Traceback (most recent call last):
>>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in
>>> __simulate
>>>    genome = Genome(pars)
>>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12,
>>> in __init__
>>>    self.createOps()
>>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 58,
>>> in createOps
>>>    self._loadData(self.filename)
>>> AttributeError: Genome instance has no attribute '_loadData'
>>>
>>> To unsubscribe from this bug, go to:
>>> https://bugs.launchpad.net/newage/+bug/598312/+subscribe
>>>
>>
>>
>> --
>> **********************************************
>> Andrés Pérez-Figueroa.
>>
>> Postdoc at
>>
>> Dep. Bioquímica, Xenética e Inmunoloxía.
>> Facultade de Bioloxía. Universidade de Vigo.
>> 36310 Vigo. Spain.
>> -------------------------------------------------------
>> web: http://webs.uvigo.es/anpefi
>> e-mail: <email address hidden>
>> Tfn/fax: [phone]
>> Skype: andres.perez.figueroa
>> **********************************************
>>
>> --
>> Error loading frecuencies from datafile
>> https://bugs.launchpad.net/bugs/598312
>> You received this bug notification because you are a member of newAge,
>> which is the registrant for newAge.
>>
>> Status in newAge: A population genetics workbench to simulate and analise age-structured populations: New
>>
>> Bug description:
>> When setting to read frecuencies from datafile it launchs this error:
>>
>> Traceback (most recent call last):
>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256, in __simulate
>>    genome = Genome(pars)
>>  File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line 12, in __init__
>>    self.createOps()
>>  File "/home/andres/tasks/Ne...

[Andrés Pérez-Figueroa (andres-perez-figueroa)]

Exactly, the SNP option has never been used.

2010/6/25 Tiago Antao <email address hidden>

> As it stands, the code only allows the load of microsatellite data,
> not SNPS, correct?
>
> 2010/6/25 Tiago Antão <email address hidden>:
> > Don't worry, I will sort this one myself.
> > I misunderstood your previous comment and thought you tried to commit.
> > The current version is probably inconsistent with your repository as I
> > have made some changes (corrected most of the bugs by now).
> >
> > Tiago
> >
> > 2010/6/25 Andrés Pérez-Figueroa <email address hidden>:
> >> push or commit?
> >>
> >> I've tried
> >>
> >> bzr commit -m "Fixed Bug: 598460" src/NewAge/Sim/LifeHistory.py
> >>
> >>
> >> but it causes:
> >> bzr: ERROR: Cannot lock
> >> LockDir(lp-69743952:///~tiagoantao/newage/trunk/.bzr/branchlock):
> Transport
> >> operation not possible: readonly transport
> >>
> >> I've already have a ssh-key in launchpad. Maybe you have to give me
> write
> >> access....
> >>
> >> 2010/6/25 Tiago Antao <email address hidden>
> >>
> >>> Don't forget to push the change so that I can see it (bzr push)
> >>>
> >>> You will probably need to set up an ssh key with launchpad
> >>>
> >>> --
> >>> Error loading frecuencies from datafile
> >>> https://bugs.launchpad.net/bugs/598312
> >>> You received this bug notification because you are a direct subscriber
> >>> of the bug.
> >>>
> >>> Status in newAge: A population genetics workbench to simulate and
> analise
> >>> age-structured populations: New
> >>>
> >>> Bug description:
> >>> When setting to read frecuencies from datafile it launchs this error:
> >>>
> >>> Traceback (most recent call last):
> >>> File "/home/andres/tasks/NewAge/soft/src/NewAge/UI/wxUI.py", line 256,
> in
> >>> __simulate
> >>> genome = Genome(pars)
> >>> File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line
> 12,
> >>> in __init__
> >>> self.createOps()
> >>> File "/home/andres/tasks/NewAge/soft/src/NewAge/Sim/Genome.py", line
> 58,
> >>> in createOps
> >>> self._loadData(self.filename)
> >>> AttributeError: Genome instance has no attribute '_loadData'
> >>>
> >>> To unsubscribe from this bug, go to:
> >>> https://bugs.launchpad.net/newage/+bug/598312/+subscribe
> >>>
> >>
> >>
> >> --
> >> **********************************************
> >> Andrés Pérez-Figueroa.
> >>
> >> Postdoc at
> >>
> >> Dep. Bioquímica, Xenética e Inmunoloxía.
> >> Facultade de Bioloxía. Universidade de Vigo.
> >> 36310 Vigo. Spain.
> >> -------------------------------------------------------
> >> web: http://webs.uvigo.es/anpefi
> >> e-mail: <email address hidden>
> >> Tfn/fax: [phone]
> >> Skype: andres.perez.figueroa
> >> **********************************************
> >>
> >> --
> >> Error loading frecuencies from datafile
> >> https://bugs.launchpad.net/bugs/598312
> >> You received this bug notification because you are a member of newAge,
> >> which is the registrant for newAge.
> >>
> >> Status in newAge: A population genetics workbench to simulate and
> analise age-structured populations: New
> >>
> >> Bug description:
> >> When setting to read frecuencies from datafile it launchs this error:
> >>
> >> Traceback ...

[Andrés Pérez-Figueroa (andres-perez-figueroa)]

2010/6/25 Tiago Antao <email address hidden>

> Don't worry, I will sort this one myself.
> I misunderstood your previous comment and thought you tried to commit.
> The current version is probably inconsistent with your repository as I
> have made some changes (corrected most of the bugs by now).
>
> Tiago
>

Ok, but note that I tried to commit the fix to bug #598460 pars without
self.pars in LifeHistory.py <https://bugs.launchpad.net/newage/+bug/598460>.
There were several pars without the self in that file and it crashed when
try to run allowing pop growth.

--
**********************************************
Andrés Pérez-Figueroa.

Postdoc at

Dep. Bioquímica, Xenética e Inmunoloxía.
Facultade de Bioloxía. Universidade de Vigo.
36310 Vigo. Spain.
-------------------------------------------------------
web: http://webs.uvigo.es/anpefi
e-mail: <email address hidden>
Tfn/fax: [phone]
Skype: andres.perez.figueroa
**********************************************