# VERSION: 2.0.0b5 (14DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_metrics from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) # Example taken from Lacy (1989), Appendix A. example = pyp_newclasses.loadPedigree(optionsfile='new_lacy.ini',debugLoad=True) example.printoptions() if example.kw['messages'] == 'verbose': print '='*80 print '[INFO]: Calling pyp_metrics.effective_founders_lacy at %s' % (pyp_nice_time()) pyp_metrics.effective_founders_lacy(example) # Example taken from Boichard et al. (1997), Figure 2 / Table II. example2a = pyp_newclasses.loadPedigree(optionsfile='new_format.ini') if example2a.kw['messages'] == 'verbose': print '='*80 print '[INFO]: Calling pyp_metrics.effective_founders_lacy at %s' % (pyp_nice_time()) pyp_metrics.effective_founders_lacy(example2a) if example2a.kw['messages'] == 'verbose': print '='*80 print 'Calling a_effective_founders_boichard() at %s' % (pyp_nice_time())
# AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal.pyp_utils import pyp_nice_time import numpy import time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) example = pyp_newclasses.loadPedigree(optionsfile='new_amatrix.ini') amatrix = pyp_newclasses.NewAMatrix(example.kw) amatrix.form_a_matrix(example.pedigree) # Here's how to save a matrix to a binary file. # amatrix.save('boichard2_pedigree.bin') # Here's how to load a matrix from a binary file. # amatrix2 = pyp_newclasses.NewAMatrix(example.kw) # amatrix2.load('boichard2_pedigree.bin') # Calculate coefficients of inbreeding on this pedigree. print '\tEntering pyp_nrm.inbreeding() at %s' % (pyp_nice_time()) example_inbreeding = pyp_nrm.inbreeding(example, method='vanraden') print '\tReturning from pyp_nrm.inbreeding() at %s' % (pyp_nice_time())
#!/usr/bin/python ############################################################################### # NAME: new_doug.py # VERSION: 2.0.0b5 (13DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_doug.ini') if example.kw['messages'] == 'verbose': print '[INFO]: Calling pyp_graphics.draw_pedigree() at %s' % (pyp_nice_time()) pyp_graphics.draw_pedigree(example, gfilename='doug_below', gtitle='Doug the German Shepherd (B)', gorient='p', gname=1, gdirec='', gfontsize=12, garrow=0, gtitloc='b') pyp_graphics.draw_pedigree(example, gfilename='doug_above', gtitle='Doug the German Shepherd (A)', gorient='p', gname=1, gdirec='', gfontsize=12, garrow=0, gtitloc='t') pyp_graphics.draw_pedigree(example, gfilename='doug_p_rl_notitle', gtitle='', gorient='p', gname=1, gdirec='RL', gfontsize=12)
#!/usr/bin/python ############################################################################### # NAME: new_graphics.py # VERSION: 2.0.0b5 (19DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_renumbering.ini') print '-'*80 print 'INFO: Pedigree ID map: %s' % (example.idmap) print '-'*80 print 'INFO: Pedigree ID reverse map: %s' % (example.backmap) print '-'*80 myinbr = pyp_nrm.inbreeding(example) print 'INFO: Coefficients of inbreeding: %s' % (myinbr) pyp_graphics.draw_pedigree(example,gfilename='new_renumbering',gtitle='My Pedigree')
# VERSION: 2.0.0b5 (19DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_metrics from PyPedal import pyp_nrm from PyPedal import pyp_utils from PyPedal.pyp_utils import pyp_nice_time if __name__=='__main__': print 'Starting pypedal.py at %s' % ( pyp_nice_time() ) example = pyp_newclasses.loadPedigree(optionsfile='new_format.ini') #pyp_utils.assign_offspring(example) #print 'First ID: %s' % ( example.kw['id_first'] ) #print 'Last ID: %s' % ( example.kw['id_last'] ) inbr, reln = inbr, reln = pyp_nrm.inbreeding(example,method='vanraden',rels=1) print 'inbr: ', inbr print 'reln: ', reln example.nrm = pyp_newclasses.NewAMatrix(example.kw) example.nrm.form_a_matrix(example.pedigree) example.nrm.save('Amatrix.txt') inbr2, reln2 = pyp_nrm.inbreeding(example,method='vanraden',rels=1) print 'inbr2: ', inbr2 print 'reln2: ', reln2
# NAME: new_reporting.py
# VERSION: 2.0.0b15 (18SE{SEPTEMBET2006)
# AUTHOR: John B. Cole, PhD ([email protected])
# LICENSE: LGPL
###############################################################################
from PyPedal import pyp_graphics
from PyPedal import pyp_jbc
from PyPedal import pyp_network
from PyPedal import pyp_newclasses
from PyPedal import pyp_nrm
from PyPedal import pyp_metrics
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(optionsfile='newfoundland.ini')
print example.idmap
print example.backmap
print example.namemap
print example.namebackmap
newf_f = pyp_nrm.inbreeding(example)
print newf_f['fx'][example.idmap[
example.namemap['Kaptn Kvols von Widdersdorf']]]
## dussel_id = example.idmap[example.namemap['King von der Dussel']]
## print 'dussel_id: ', dussel_id
##
## print 'Empirical proof that ancestor loss coefficients are the same'
## print 'as pedigree completeness.'
from PyPedal import pyp_newclasses
from PyPedal import pyp_network
from PyPedal.pyp_utils import pyp_nice_time
try:
import networkx
except ImportError:
logging.error('The networkx module could not be imported in pyp_network. Routines using networkx functionality are not available.')
if __name__=='__main__':
print 'Starting pypedal.py at %s' % ( pyp_nice_time() )
print '\tLoading pedigree at %s' % ( pyp_nice_time() )
example = pyp_newclasses.loadPedigree(optionsfile='new_networkx.ini')
print 'Calling pyp_network.ped_to_graph()'
ng = pyp_network.ped_to_graph(example)
# print 'The graph has %d nodes' % len(ng.nodes())
# print ng.nodes()
# print ng.edges()
#
## print 'Drawing graph madeup.ps'
## networkx.drawing.draw(ng)
## networkx.drawing.savefig("madeup.ps")
##
## print 'Drawing graph madeup.dot'
## networkx.drawing.write_dot(ng,path="madeup.dot")
## networkx.drawing.draw_nxpydot(ng)
options = {}
options['pedfile'] = 'new_amatrix.ped'
options['pedname'] = 'A Large Dog Pedigree'
options['pedformat'] = 'asdgb'
options['messages'] = 'verbose'
options['renumber'] = 1
if __name__ == '__main__':
print 'Starting pypedal.py at %s' % (pyp_utils.pyp_nice_time())
# example is a PyPedal NewPedigree object that stores the individual
# animal records, as well as other information about the pedigree.
# Most things are done by calling methods on example, or by passing
# it to functions.
example = pyp_newclasses.loadPedigree(optionsfile='new_amatrix.ini')
# We're going to create an instance of the NewAMatrix class, which we
# can use to store relationship matrices, and then create the A matrix
# from the pedigree stored in example. Note that we can only store
# matrices that we can allocate in memory!
amatrix = pyp_newclasses.NewAMatrix(example.kw)
amatrix.form_a_matrix(example.pedigree)
# Here's how to save the A matrix to a binary file.
amatrix.save('boichard2_pedigree.bin')
# Here's how to load the A matrix from a binary file.
amatrix2 = pyp_newclasses.NewAMatrix(example.kw)
amatrix2.load('boichard2_pedigree.bin')
# NAME: new_reporting.py
# VERSION: 2.0.0b15 (18SE{SEPTEMBET2006)
# AUTHOR: John B. Cole, PhD ([email protected])
# LICENSE: LGPL
###############################################################################
from PyPedal import pyp_graphics
from PyPedal import pyp_jbc
from PyPedal import pyp_network
from PyPedal import pyp_newclasses
from PyPedal import pyp_nrm
from PyPedal import pyp_metrics
if __name__ == '__main__':
example = pyp_newclasses.loadPedigree(optionsfile='newfoundland.ini')
print example.idmap
print example.backmap
print example.namemap
print example.namebackmap
newf_f = pyp_nrm.inbreeding(example)
print newf_f['fx'][example.idmap[example.namemap['Kaptn Kvols von Widdersdorf']]]
## dussel_id = example.idmap[example.namemap['King von der Dussel']]
## print 'dussel_id: ', dussel_id
##
## print 'Empirical proof that ancestor loss coefficients are the same'
## print 'as pedigree completeness.'
##
options = {}
options['messages'] = 'verbose'
options['renumber'] = 1
#options['pedfile'] = 'new_renumbering.ped'
options['pedfile'] = 'mrode.ped'
#options['pedformat'] = 'asdgb'
options['pedformat'] = 'asd'
options['pedname'] = 'My Pedigree'
options['matrix_type'] = 'sparse'
options['renumber'] = 0
options['pedigree_is_renumbered'] = 1
if __name__ == '__main__':
# example = pyp_newclasses.loadPedigree(optionsfile='new_inbreeding.ini')
example = pyp_newclasses.loadPedigree(options)
print example
print '[DEBUG]: matrix_type = ', example.kw['matrix_type']
print 'Started computing inbreeding at %s' % (pyp_nice_time())
example_inbreeding_vr = pyp_nrm.inbreeding(example, method='vanraden')
example_inbreeding_ml = pyp_nrm.inbreeding(example, method='meu_luo')
example_inbreeding_qu = pyp_nrm.inbreeding(example, method='mod_meu_luo')
print 'Finished computing inbreeding at %s' % (pyp_nice_time())
# print example_inbreeding
# print example_inbreeding['fx'][28]
print '\nVanRaden : ', example_inbreeding_vr['metadata']
print '\nMeuwissen and Luo : ', example_inbreeding_ml['metadata']
print '\nModified Meuwissen and Luo: ', example_inbreeding_qu['metadata']
# NAME: new_reporting.py # VERSION: 2.0.0b7 (11APRIL2006) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_network from PyPedal import pyp_newclasses from PyPedal import pyp_nrm #from PyPedal import pyp_reports from PyPedal import pyp_metrics if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_reporting.ini') #example.printoptions() #pyp_reports.pdfPedigreeMetadata(example, titlepage = 1, reporttitle = 'Metadada for My Pedigree', reportauthor = 'John B. Cole, PhD') #pyp_reports.pdfPedigreeMetadata(example, titlepage = 1, reportauthor = 'John B. Cole, PhD', reportfile = 'metadata_report.pdf') ib = pyp_nrm.inbreeding(example) #coi_by_year = pyp_reports.meanMetricBy(example,metric='fa',byvar='by',createpdf=1) #coi_by_year #print ib #for _e in example.pedigree: #print _e.name, _e.fa print example.kw['paper_size']
#!/usr/bin/python ############################################################################### # NAME: new_subpedigree.py # VERSION: 2.0.0b14 (16MAY2006) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_utils from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_subpedigree.ini') print '='*70 keepid = [] for k in ['Clover','Dewey','Wicket']: ped = pyp_nrm.recurse_pedigree(example,example.idmap[example.namemap[k]],[]) for p in ped: if p.animalID not in keepid: keepid.append(p.animalID) if example.idmap[example.namemap[k]] not in keepid: keepid.append(example.idmap[example.namemap[k]]) example2 = pyp_utils.subpedigree(example,keepid) example2.metadata.printme()
############################################################################### # NAME: new_graphics3.py # VERSION: 2.0.0b15 (18SEPTEMBER2006) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_demog from PyPedal import pyp_graphics from PyPedal import pyp_jbc from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_metrics from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) example = pyp_newclasses.loadPedigree(optionsfile='new_graphics3.ini') if example.kw['messages'] == 'verbose': print '[INFO]: Calling pyp_graphics.new_draw_pedigree() at %s' % ( pyp_nice_time()) pyp_graphics.new_draw_pedigree(example, gfilename='graphics3', gtitle='graphics3 pedigree', gorient='p') pyp_jbc.color_pedigree(example,gfilename='graphics3', ghatch='0', \ metric='sons', gtitle='Nodes are colored by number of sons.', \ gprog='dot', gname=1)
############################################################################### # NAME: new_amatrix.py # VERSION: 2.0.0rc7 (07MAY2008) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal.pyp_utils import pyp_nice_time import numpy import time options = {} options['messages'] = 'verbose' options['pedfile'] = 'vizsla_ped3.csv' options['pedformat'] = 'asd' options['reorder'] = 1 options['reorder_max_rounds'] = 1000 options['has_header'] = 1 options['sepchar'] = ',' options['pedname'] = 'Viszla Pedigree' options['debug_messages'] = 0 if __name__ == '__main__': print 'PyPedal started at %s' % (pyp_nice_time()) viszla = pyp_newclasses.loadPedigree(options, debugLoad=True) print 'PyPedal stopped at %s' % (pyp_nice_time())
# print '\n3 gen inbreeding: %s' % ( example_inbreeding )
# print '\nMean 3 gen CoI: %s' % ( example_inbreeding['metadata']['all']['f_avg'] )
# This is an advanced example that uses dict4ini to read
# configurations for multiple pedigrees from the same file.
from PyPedal import dict4ini
import sys
kw_all = dict4ini.DictIni('new_inbreeding2multiple.ini')
if len(kw_all) == 0:
sys.exit(0)
kw_all = kw_all.dict()
kw_noinbred = kw_all['noinbreeding']
kw_horse = kw_all['horse']
# noinbred = pyp_newclasses.loadPedigree(kw_noinbred)
horse = pyp_newclasses.loadPedigree(kw_horse)
# noinbred_inbreeding = pyp_nrm.inbreeding(noinbred, method='vanraden', gens=3)
# print '\nNoinbred 3 gen inbreeding: %s' % ( noinbred_inbreeding )
# print '\nNoinbred mean 3 gen CoI: %s' % ( noinbred_inbreeding['metadata']['all']['f_avg'] )
#
# pyp_graphics.draw_pedigree(horse, gfilename='blue_joe',
# gtitle='Blue Joe\'s Pedigree', gorient='p', gname=1, gdirec='RL',
# gfontsize=12, garrow=0, gtitloc='b')
## print '\nRen ID\tName\n------\t----'
## for _k in horse.backmap.keys():
## print '%s\t%s' % ( _k, horse.pedigree[int(_k)-1].name )
## print '-'*80
options = {}
options['messages'] = 'verbose'
options['renumber'] = 1
#options['pedfile'] = 'new_renumbering.ped'
options['pedfile'] = 'mrode.ped'
#options['pedformat'] = 'asdgb'
options['pedformat'] = 'asd'
options['pedname'] = 'My Pedigree'
options['matrix_type'] = 'sparse'
options['renumber'] = 0
options['pedigree_is_renumbered'] = 1
if __name__ == '__main__':
# example = pyp_newclasses.loadPedigree(optionsfile='new_inbreeding.ini')
example = pyp_newclasses.loadPedigree(options)
print example
print '[DEBUG]: matrix_type = ', example.kw['matrix_type']
print 'Started computing inbreeding at %s' % (pyp_nice_time())
example_inbreeding_vr = pyp_nrm.inbreeding(example,method='vanraden')
example_inbreeding_ml = pyp_nrm.inbreeding(example,method='meu_luo')
example_inbreeding_qu = pyp_nrm.inbreeding(example,method='mod_meu_luo')
print 'Finished computing inbreeding at %s' % (pyp_nice_time())
# print example_inbreeding
# print example_inbreeding['fx'][28]
print '\nVanRaden : ', example_inbreeding_vr['metadata']
print '\nMeuwissen and Luo : ', example_inbreeding_ml['metadata']
print '\nModified Meuwissen and Luo: ', example_inbreeding_qu['metadata']
# LICENSE: LGPL
###############################################################################
from PyPedal import pyp_newclasses
from PyPedal.pyp_utils import pyp_nice_time
if __name__ == '__main__':
print 'Starting pypedal.py at %s' % (pyp_nice_time())
print '=' * 80
# This should fail because we are providing neither a dictionary
# of options or a configuration file name.
print 'This load should fail'
myped1 = pyp_newclasses.loadPedigree()
print myped1
print '-' * 80
# This should fail because we are providing an empty dictionary
# and there is no configuration file named pypedal.ini in the
# examples directory.
options = {}
print 'This load should fail'
myped2 = pyp_newclasses.loadPedigree(options)
print myped2
print '-' * 80
# This should work because we are providing a dictionary of
# VERSION: 2.0.0b5 (14DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_metrics from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) # Example taken from Lacy (1989), Appendix A. example = pyp_newclasses.loadPedigree(optionsfile='new_lacy.ini', debugLoad=True) example.printoptions() if example.kw['messages'] == 'verbose': print '=' * 80 print '[INFO]: Calling pyp_metrics.effective_founders_lacy at %s' % ( pyp_nice_time()) pyp_metrics.effective_founders_lacy(example) # Example taken from Boichard et al. (1997), Figure 2 / Table II. example2a = pyp_newclasses.loadPedigree(optionsfile='new_format.ini') if example2a.kw['messages'] == 'verbose': print '=' * 80 print '[INFO]: Calling pyp_metrics.effective_founders_lacy at %s' % ( pyp_nice_time()) pyp_metrics.effective_founders_lacy(example2a) if example2a.kw['messages'] == 'verbose':
#!/usr/bin/python ############################################################################### # NAME: new_format.py # VERSION: 2.0.0b5 (13DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses if __name__ == '__main__': # Example taken from Boichard et al. (1997), Figure 2 / Table II. example2a = pyp_newclasses.loadPedigree(optionsfile='new_format.ini') example2a.metadata.printme()
from PyPedal import pyp_newclasses
from PyPedal import pyp_metrics
from PyPedal import pyp_nrm
from PyPedal import pyp_io
from PyPedal import pyp_graphics
options = {}
# This is the name of the input tile.
options['pedfile'] = ''
# This is a descriptor used in some output.
options['pedname'] = 'Text Stream'
# Don't mess with these options.
options['messages'] = 'verbose'
options['renumber'] = 1
options['pedformat'] = 'ASD'
options['assign_sexes'] = 1
if __name__ == "__main__":
pedstream = 'a1,s1,d1\na2,s2,d2\na3,a1,a2\n'
test = pyp_newclasses.loadPedigree(options,pedsource='textstream',pedstream=pedstream)
test.kw['database_name'] = 'test_pypedal_save'
test.kw['dbtable_name'] = 'test'
test.savedb(drop=True)
test2 = pyp_newclasses.loadPedigree(options,pedsource='db')
test2.metadata.printme()
test2.savegraph(pedoutfile='test.adj')
# NAME: new_graphics.py # VERSION: 2.0.0b5 (13DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_db from PyPedal import pyp_graphics from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal import pyp_reports from PyPedal.pyp_utils import pyp_nice_time if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_graphics.ini') # example_inbreeding = pyp_nrm.inbreeding(example) pyp_graphics.rmuller_spy_matrix_pil(example.nrm.nrm, fname='dog_sparsity.png', cutoff=0.01, do_outline=0, height=example.nrm.nrm.shape[0], width=example.nrm.nrm.shape[0]) pyp_graphics.rmuller_pcolor_matrix_pil(example.nrm.nrm, fname='dog_long_pcolored.png', do_outline=0, height=example.nrm.nrm.shape[0], width=example.nrm.nrm.shape[0]) #pyp_db.loadPedigreeTable(example) pyp_db.deleteTable(example) pyp_db.populatePedigreeTable(example) coi_by_year = pyp_reports.meanMetricBy(example, metric='fa', byvar='by') print 'coi_by_year: ', coi_by_year cby = coi_by_year del(cby[1900]) pyp_graphics.plot_line_xy(coi_by_year, gfilename='dog_coi_by_year', gtitle='', gxlabel='Birth year', gylabel='Coefficient of inbreeding')
#!/usr/bin/python ############################################################################### # NAME: new_simulate.py # VERSION: 2.0.0b15 (08JUNE2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_graphics from PyPedal import pyp_network import networkx if __name__ == '__main__': for i in range(1): print 'Simulating and drawing pedigree %d' % ( i ) example = pyp_newclasses.loadPedigree(optionsfile='new_simulate.ini') print example
# NAME: new_simulate.py # VERSION: 2.0.0b15 (08JUNE2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_graphics from PyPedal import pyp_network import networkx if __name__ == '__main__': for i in range(1): print 'Simulating and drawing pedigree %d' % (i) example = pyp_newclasses.loadPedigree(optionsfile='new_simulate.ini') print example #_gfn = 'simulated_pedigree_%d' % ( i ) _gfn = 'simulated_pedigree' _gt = 'Simulated Pedigree %d' % (i) pyp_graphics.draw_pedigree(example, gfilename=_gfn, gtitle=_gt, gformat='ps', garrow=0, gclusters=0) #print 'Animal\tOriginal\tSire\tDam\tSex\tGen' #for _p in example.pedigree: #print '%s\t%s\t\t%s\t%s\t%s\t%s' % ( _p.animalID, _p.originalID, _p.sireID, _p.damID, _p.sex, _p.gen )
from PyPedal import pyp_nrm
from PyPedal import pyp_io
from PyPedal import pyp_graphics
options = {}
# This is the name of the input tile.
options['pedfile'] = ''
# This is a descriptor used in some output.
options['pedname'] = 'Text Stream'
# Don't mess with these options.
options['messages'] = 'verbose'
options['renumber'] = 1
options['pedformat'] = 'ASD'
options['assign_sexes'] = 1
if __name__ == "__main__":
pedstream = 'a1,s1,d1\na2,s2,d2\na3,a1,a2\n'
test = pyp_newclasses.loadPedigree(options,
pedsource='textstream',
pedstream=pedstream)
test.kw['database_name'] = 'test_pypedal_save'
test.kw['dbtable_name'] = 'test'
test.savedb(drop=True)
test2 = pyp_newclasses.loadPedigree(options, pedsource='db')
test2.metadata.printme()
test2.savegraph(pedoutfile='test.adj')
#!/usr/bin/python ############################################################################### # NAME: new_ids.py # VERSION: 2.0.0b5 (14DECEMBER2005) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses if __name__ == '__main__': example = pyp_newclasses.loadPedigree(optionsfile='new_ids.ini') for _p in example.pedigree: _p.printme()
# LICENSE: LGPL
###############################################################################
from PyPedal import pyp_newclasses
from PyPedal.pyp_utils import pyp_nice_time
if __name__=='__main__':
print 'Starting pypedal.py at %s' % (pyp_nice_time())
print '='*80
# This should fail because we are providing neither a dictionary
# of options or a configuration file name.
print 'This load should fail'
myped1 = pyp_newclasses.loadPedigree()
print myped1
print '-'*80
# This should fail because we are providing an empty dictionary
# and there is no configuration file named pypedal.ini in the
# examples directory.
options = {}
print 'This load should fail'
myped2 = pyp_newclasses.loadPedigree(options)
print myped2
print '-'*80
# This should work because we are providing a dictionary of
############################################################################### # NAME: new_amatrix.py # VERSION: 2.0.0rc7 (07MAY2008) # AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal.pyp_utils import pyp_nice_time import numpy import time options = {} options['messages'] = 'verbose' options['pedfile'] = 'vizsla_ped3.csv' options['pedformat'] = 'asd' options['reorder'] = 1 options['reorder_max_rounds'] = 1000 options['has_header'] = 1 options['sepchar'] = ',' options['pedname'] = 'Viszla Pedigree' options['debug_messages'] = 0 if __name__ == '__main__': print 'PyPedal started at %s' % (pyp_nice_time()) viszla = pyp_newclasses.loadPedigree(options, debugLoad=True) print 'PyPedal stopped at %s' % (pyp_nice_time())
# AUTHOR: John B. Cole, PhD ([email protected]) # LICENSE: LGPL ############################################################################### from PyPedal import pyp_newclasses from PyPedal import pyp_nrm from PyPedal.pyp_utils import pyp_nice_time import numpy import numpy.linalg import time if __name__ == '__main__': print 'Starting pypedal.py at %s' % (pyp_nice_time()) example = pyp_newclasses.loadPedigree(optionsfile='new_decompose.ini') amatrix = pyp_newclasses.NewAMatrix(example.kw) amatrix.form_a_matrix(example.pedigree) print '-'*80 print 'Calling a_decompose()' print '=====================' D, T = pyp_nrm.a_decompose(example) print 'D: ', D print 'T: ', T print '-'*80 print 'Calculating Ainv from D and T' print '=============================' l = example.metadata.num_records Tinv = numpy.linalg.inv(T)