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')
pyp_graphics.draw_pedigree(example, gfilename='dog_pedigree', gtitle='Dog pedigree',gformat='jpg',gsize='f')
pyp_graphics.plot_founders_by_year(example, gfilename='dog_founders_by_year', gtitle='Number of founders within each birthyear')
from PyPedal import pyp_graphics
from PyPedal import pyp_newclasses
from PyPedal import pyp_nrm
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_classes.ini')
if example.kw['messages'] == 'verbose':
print '[INFO]: Forming numerator relationship matrix at %s' % ( pyp_nice_time() )
my_a = pyp_nrm.fast_a_matrix_r(example.pedigree,example.kw)
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM sparsity at %s' % ( pyp_nice_time() )
pyp_graphics.rmuller_spy_matrix_pil(my_a,fname='boichard2_spy.png')
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM in pseudocolor at %s' % ( pyp_nice_time() )
pyp_graphics.rmuller_pcolor_matrix_pil(my_a,fname='boichard2_pcolor.png')
pyp_graphics.draw_pedigree(example, gfilename='boichard2_pedigree', \
gtitle='', gorient='p', gdirec='RL', gfontsize=12)
print 'Stopping pypedal.py at %s' % ( 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')
from PyPedal import pyp_nrm
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_classes.ini')
if example.kw['messages'] == 'verbose':
print '[INFO]: Forming numerator relationship matrix at %s' % (
pyp_nice_time())
my_a = pyp_nrm.fast_a_matrix_r(example.pedigree, example.kw)
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM sparsity at %s' % (pyp_nice_time())
pyp_graphics.rmuller_spy_matrix_pil(my_a, fname='boichard2_spy.png')
if example.kw['messages'] == 'verbose':
print '[INFO]: Visualizing NRM in pseudocolor at %s' % (
pyp_nice_time())
pyp_graphics.rmuller_pcolor_matrix_pil(my_a, fname='boichard2_pcolor.png')
pyp_graphics.draw_pedigree(example, gfilename='boichard2_pedigree', \
gtitle='', gorient='p', gdirec='RL', gfontsize=12)
print 'Stopping pypedal.py at %s' % (pyp_nice_time())
