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License: GNU General Public License v2.0
2.0
License: GNU General Public License v2.0
I thought that this project was dead (from sourceforge) and was happy to find it on github. However, no release has been made since 2012 and python setup.py install
failed under Python 3.8.
If this package is no longer maintained, perhaps @wintermind can put the repo in archive mode.
These files and directory
https://github.com/wintermind/pypedal/tree/master/PyPedal.egg-info
are already generated and don't need to be here.
Also these one here:
https://github.com/wintermind/pypedal/tree/master/PyPedal/PyPedal.egg-info
Old link
http://www.pfdubois.com/numpy/
goes to a 404 page
Updated link
http://numpy.scipy.org/
Right now, the only way to do this is using the form_nrm keyword. That's fine for small pedigrees, and really slow for large ones. It would be nice if you could tell PyPedal to load the pedigree, and as part of the loading process compute the CoI and store them in the pedigree. Note that it is important that the method for computing inbreeding be user-specifiable.
The downside is that this will require some work, and will save only one line of code for the user.
I'm struggling to get my head around how I can load a pedigree from sqlite.
Where do I enter the name of the animal I want to retrieve from the database?
Lets say I want to run the below script, I'm looking for a horse in my database called Verve (there is more than one horse with this name also).
from PyPedal import pyp_newclasses
options = {}
options['messages'] = 'verbose'
options['pedfile'] = 'Verve.ped'
options['pedformat'] = 'ASDx'
options['database_name'] = 'pypedal'
options['dbtable_name'] = 'horses_pp'
options['database_type'] = 'sqlite'
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(options,pedsource='db')
example.metadata.printme()
I have imported my data into the default sqlite database for PyPedal
animalID integer UNIQUE, animalName varchar(128), sireID integer, damID integer, generation real, infGeneration real, birthyear integer, sex char(1), coi real, founder char(1), ancestor char(1), originalID text, renumberedID integer, pedgreeComp real, breed text, age real, alive char(1), num_sons integer, num_daus integer, num_unk integer
"122499" "164141" "Verve" "41674" "103037" "NULL" "NULL" "2001" "D" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL" "NULL"
Here you got a bug report.
I am using your program for our old homestead rabbits Gotlandskanin here in Sweden.
I would like to calculate inbreed. But I got the following error.
File "gottis.py", line 32, in <module>
print pyp_metrics.mating_coi(test.idmap[test.namemap['1158-1624']],test.idmap[test.namemap['1115-1528']],test)
File "build/bdist.linux-x86_64/egg/PyPedal/pyp_metrics.py", line 1574, in mating_coi
TypeError: cannot concatenate 'str' and 'int' objects
I basically just load the pedigree and then try to calculate.
test = pyp_newclasses.loadPedigree(options)
print test
print pyp_metrics.mating_coi(test.idmap[test.namemap['1158-1624']],test.idmap[test.namemap['1115-1528']],test)
Running the git version from main branch
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