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pypedal's Introduction

README - PyPedal Version 2.0.4
-------------------------------------------------

WHAT IS PyPedal?

PyPedal is a Python package for pedigree analysis.  PyPedal is a research tool
for the use of the author and any others who might be interested in its use. It
was originally developed by John B. Cole, and may be freely (re)distributed.

DOCUMENTATION

Limited (read preliminary) documentation is available in TeX and Postscript
format in this repository. An HTML version of the manual also may be found at:
http://pypedal.sourceforge.net/.

INSTALLING PyPedal

You should be able to use the usual setup.py installer that's included in the
download.

You must have Python 2.7 (or later) installed in order to use PyPedal. PyPedal
depends on features in 2.7 that are not present in earlier versions of Python.
You may find Python for your operating system at: http://www.python.org/.

You must have the NumPy extension to Python installed.  You can obtain NumPy as
well as installation instructions, at: http://www.numpy.org/.

I've successfully used PyPedal in various flavors of RedHat Linux (including
RHEL), Mandrake Linux, CentOS, and macOS (including Big Sur). I don't routinely
use Windows, so I'm afraid I can't be too much help there.

REPORTING BUGS

To report a bug in PyPedal, please open an issue on GitHub:
https://github.com/wintermind/pypedal.

For general support and questions, please e-mail the author at
[email protected].


TRADEMARKS

Microsoft and Windows are registered trademarks of Microsoft Corporation. UNIX
is a registered trademark of the X/Open Group, Inc.  Linux is a registered
trademark of Linus Torvalds.


COPYRIGHT

PyPedal is copyright 2001-2022 by John B. Cole ([email protected];
http://johnbcole.com/).

LICENSING

PyPedal is available under the terms of the GNU Library General Public License
v2.0.

pypedal's People

Contributors

sam-m888 avatar wintermind avatar

Stargazers

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Watchers

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Forkers

pjmartinez improvestats mweitzel pqyplzxhgf hugo-toledo oogiem sam-m888

pypedal's Issues

Python 3 compatibility

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If this package is no longer maintained, perhaps @wintermind can put the repo in archive mode.

Problems with pyp_metrics.mating_coi

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

Shortcut for computing inbreeding when creating/loading pedigree

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.

Confusion regarding loading pedigree from database

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"

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