class Simulation(object):
def __init__(self):
self.markerSetBuilder = MarkerSetBuilder()
self.img = IMG()
def run(self):
print('\n Reading reference genome tree.')
treeFile = os.path.join(os.path.dirname(sys.argv[0]), '..', 'data',
'genome_tree', 'genome_tree_prok.refpkg',
'genome_tree.final.tre')
tree = dendropy.Tree.get_from_path(treeFile,
schema='newick',
as_rooted=True,
preserve_underscores=True)
# get all Finished, Trusted genomes
metadata = self.img.genomeMetadata()
bacteriaIds = self.img.getGenomesByClade('domain', 'Bacteria',
metadata)
print('# Bacteria: %d' % len(bacteriaIds))
start = time.time()
#self.markerSetBuilder.cachedGeneCountTable = self.img.geneCountTable(metadata.keys())
end = time.time()
print('globalGeneCountTable: %.2f' % (end - start))
start = time.time()
#self.markerSetBuilder.precomputeGenomeSeqLens(metadata.keys())
end = time.time()
print('precomputeGenomeSeqLens: %.2f' % (end - start))
start = time.time()
#self.markerSetBuilder.precomputeGenomeFamilyPositions(metadata.keys(), 5000)
end = time.time()
print('precomputeGenomeFamilyPositions: %.2f' % (end - start))
#start = time.time()
#test = self.img.geneDistTable(metadata.keys(), self.markerSetBuilder.globalGeneCountTable.keys(), spacingBetweenContigs=1e6)
#end = time.time()
#print 'geneDistTable: %.2f' % (end - start)
#t = raw_input('waiting...')
start = time.time()
#testGenomeId = archaeaIds.pop()
#testNode = tree.find_node_with_taxon_label('IMG_' + testGenomeId)
#binMarkerSets, refinedBinMarkerSet = self.markerSetBuilder.buildBinMarkerSet(tree, testNode.parent_node, 0.97, 0.97, bMarkerSet = True)
markerSet = self.markerSetBuilder.buildMarkerSet(
bacteriaIds, 0.97, 0.97)
end = time.time()
print('buildMarkerSet: %.2f' % (end - start))
print(len(markerSet.markerSet))
test = eval(
"[set(['TIGR01080', 'pfam08071', 'pfam00900']), set(['pfam08069', 'pfam00312']), set(['pfam00276', 'pfam00573', 'pfam00297']), set(['pfam00333', 'pfam00327', 'pfam03719']), set(['pfam04563', 'pfam04560', 'pfam04983', 'pfam04566', 'pfam04567', 'pfam04565', 'pfam04997', 'pfam00562', 'pfam05000', 'pfam00623', 'pfam01191', 'pfam04561', 'TIGR02389']), set(['pfam00831', 'pfam01868', 'pfam00189', 'pfam00237']), set(['pfam01280', 'pfam00861', 'pfam01655']), set(['pfam01194', 'pfam00380', 'pfam00572']), set(['TIGR00425', 'pfam08068']), set(['pfam01157', 'pfam03874']), set(['pfam00416', 'TIGR01018']), set(['pfam00679', 'pfam03764']), set(['TIGR00344', 'TIGR03683']), set(['pfam01193', 'pfam01000']), set(['pfam00750', 'pfam05746']), set(['pfam00935', 'pfam01667']), set(['pfam00867', 'pfam00752']), set(['pfam01172', 'pfam09377']), set(['pfam03950', 'pfam00749']), set(['pfam00181', 'pfam03947']), set(['pfam00687', 'pfam00466']), set(['TIGR03679', 'TIGR00289']), set(['pfam01198', 'pfam01912']), set(['pfam00673', 'pfam00281']), set(['TIGR00134']), set(['pfam00410']), set(['pfam00411']), set(['pfam01090']), set(['pfam01092']), set(['pfam04919']), set(['TIGR00336']), set(['pfam01864']), set(['TIGR00442']), set(['pfam01866']), set(['pfam01780']), set(['TIGR01046']), set(['pfam00318']), set(['pfam00252']), set(['pfam09173']), set(['pfam00238']), set(['pfam01798']), set(['pfam01246']), set(['pfam07541']), set(['pfam00736']), set(['TIGR00522']), set(['pfam01269']), set(['TIGR00329']), set(['pfam01015']), set(['TIGR00392']), set(['pfam00203']), set(['TIGR00398']), set(['pfam01725']), set(['pfam02005']), set(['TIGR00422']), set(['pfam03439']), set(['pfam01351']), set(['pfam01922']), set(['pfam11987']), set(['pfam04127']), set(['TIGR00064']), set(['TIGR00389']), set(['pfam13656']), set(['pfam00298']), set(['TIGR00432']), set(['TIGR03677']), set(['pfam00958']), set(['pfam05221']), set(['pfam00347']), set(['TIGR03685']), set(['pfam03876']), set(['pfam01192']), set(['pfam01984']), set(['pfam00827']), set(['pfam01982']), set(['pfam01981']), set(['TIGR00408']), set(['TIGR00270']), set(['TIGR03665']), set(['pfam02978']), set(['pfam03484']), set(['pfam01201']), set(['TIGR02076']), set(['pfam00832']), set(['pfam00833']), set(['TIGR00419']), set(['pfam00177']), set(['pfam06418']), set(['TIGR00057']), set(['TIGR00549']), set(['pfam13685']), set(['pfam05670']), set(['pfam01849']), set(['TIGR02338']), set(['TIGR00468']), set(['pfam09249']), set(['pfam01287']), set(['pfam00164']), set(['pfam01282']), set(['TIGR03724']), set(['pfam01200']), set(['TIGR02153']), set(['TIGR00670']), set(['pfam00398']), set(['TIGR01213']), set(['pfam06026']), set(['pfam04019']), set(['pfam04010']), set(['pfam00366'])]"
)
print(len(test))
for ms in markerSet.markerSet:
bMatch = False
for tms in test:
if tms == ms:
print(ms)
print(tms)
print('---------')
bMatch = True
break
if not bMatch:
print('BOO!')
if str(
markerSet.markerSet
) == "[set(['TIGR01080', 'pfam08071', 'pfam00900']), set(['pfam08069', 'pfam00312']), set(['pfam00276', 'pfam00573', 'pfam00297']), set(['pfam00333', 'pfam00327', 'pfam03719']), set(['pfam04563', 'pfam04560', 'pfam04983', 'pfam04566', 'pfam04567', 'pfam04565', 'pfam04997', 'pfam00562', 'pfam05000', 'pfam00623', 'pfam01191', 'pfam04561', 'TIGR02389']), set(['pfam00831', 'pfam01868', 'pfam00189', 'pfam00237']), set(['pfam01280', 'pfam00861', 'pfam01655']), set(['pfam01194', 'pfam00380', 'pfam00572']), set(['TIGR00425', 'pfam08068']), set(['pfam01157', 'pfam03874']), set(['pfam00416', 'TIGR01018']), set(['pfam00679', 'pfam03764']), set(['TIGR00344', 'TIGR03683']), set(['pfam01193', 'pfam01000']), set(['pfam00750', 'pfam05746']), set(['pfam00935', 'pfam01667']), set(['pfam00867', 'pfam00752']), set(['pfam01172', 'pfam09377']), set(['pfam03950', 'pfam00749']), set(['pfam00181', 'pfam03947']), set(['pfam00687', 'pfam00466']), set(['TIGR03679', 'TIGR00289']), set(['pfam01198', 'pfam01912']), set(['pfam00673', 'pfam00281']), set(['TIGR00134']), set(['pfam00410']), set(['pfam00411']), set(['pfam01090']), set(['pfam01092']), set(['pfam04919']), set(['TIGR00336']), set(['pfam01864']), set(['TIGR00442']), set(['pfam01866']), set(['pfam01780']), set(['TIGR01046']), set(['pfam00318']), set(['pfam00252']), set(['pfam09173']), set(['pfam00238']), set(['pfam01798']), set(['pfam01246']), set(['pfam07541']), set(['pfam00736']), set(['TIGR00522']), set(['pfam01269']), set(['TIGR00329']), set(['pfam01015']), set(['TIGR00392']), set(['pfam00203']), set(['TIGR00398']), set(['pfam01725']), set(['pfam02005']), set(['TIGR00422']), set(['pfam03439']), set(['pfam01351']), set(['pfam01922']), set(['pfam11987']), set(['pfam04127']), set(['TIGR00064']), set(['TIGR00389']), set(['pfam13656']), set(['pfam00298']), set(['TIGR00432']), set(['TIGR03677']), set(['pfam00958']), set(['pfam05221']), set(['pfam00347']), set(['TIGR03685']), set(['pfam03876']), set(['pfam01192']), set(['pfam01984']), set(['pfam00827']), set(['pfam01982']), set(['pfam01981']), set(['TIGR00408']), set(['TIGR00270']), set(['TIGR03665']), set(['pfam02978']), set(['pfam03484']), set(['pfam01201']), set(['TIGR02076']), set(['pfam00832']), set(['pfam00833']), set(['TIGR00419']), set(['pfam00177']), set(['pfam06418']), set(['TIGR00057']), set(['TIGR00549']), set(['pfam13685']), set(['pfam05670']), set(['pfam01849']), set(['TIGR02338']), set(['TIGR00468']), set(['pfam09249']), set(['pfam01287']), set(['pfam00164']), set(['pfam01282']), set(['TIGR03724']), set(['pfam01200']), set(['TIGR02153']), set(['TIGR00670']), set(['pfam00398']), set(['TIGR01213']), set(['pfam06026']), set(['pfam04019']), set(['pfam04010']), set(['pfam00366'])]":
print('Good to go!')
else:
print('oh, shit!!!!')
class Simulation(object):
def __init__(self):
self.markerSetBuilder = MarkerSetBuilder()
self.img = IMG()
def run(self):
print '\n Reading reference genome tree.'
treeFile = os.path.join(os.path.dirname(sys.argv[0]), '..', 'data', 'genome_tree', 'genome_tree_prok.refpkg', 'genome_tree.final.tre')
tree = dendropy.Tree.get_from_path(treeFile, schema='newick', as_rooted=True, preserve_underscores=True)
# get all Finished, Trusted genomes
metadata = self.img.genomeMetadata()
bacteriaIds = self.img.getGenomesByClade('domain', 'Bacteria', metadata)
print '# Bacteria: %d' % len(bacteriaIds)
start = time.time()
#self.markerSetBuilder.cachedGeneCountTable = self.img.geneCountTable(metadata.keys())
end = time.time()
print 'globalGeneCountTable: %.2f' % (end - start)
start = time.time()
#self.markerSetBuilder.precomputeGenomeSeqLens(metadata.keys())
end = time.time()
print 'precomputeGenomeSeqLens: %.2f' % (end - start)
start = time.time()
#self.markerSetBuilder.precomputeGenomeFamilyPositions(metadata.keys(), 5000)
end = time.time()
print 'precomputeGenomeFamilyPositions: %.2f' % (end - start)
#start = time.time()
#test = self.img.geneDistTable(metadata.keys(), self.markerSetBuilder.globalGeneCountTable.keys(), spacingBetweenContigs=1e6)
#end = time.time()
#print 'geneDistTable: %.2f' % (end - start)
#t = raw_input('waiting...')
start = time.time()
#testGenomeId = archaeaIds.pop()
#testNode = tree.find_node_with_taxon_label('IMG_' + testGenomeId)
#binMarkerSets, refinedBinMarkerSet = self.markerSetBuilder.buildBinMarkerSet(tree, testNode.parent_node, 0.97, 0.97, bMarkerSet = True)
markerSet = self.markerSetBuilder.buildMarkerSet(bacteriaIds, 0.97, 0.97)
end = time.time()
print 'buildMarkerSet: %.2f' % (end - start)
print len(markerSet.markerSet)
test = eval("[set(['TIGR01080', 'pfam08071', 'pfam00900']), set(['pfam08069', 'pfam00312']), set(['pfam00276', 'pfam00573', 'pfam00297']), set(['pfam00333', 'pfam00327', 'pfam03719']), set(['pfam04563', 'pfam04560', 'pfam04983', 'pfam04566', 'pfam04567', 'pfam04565', 'pfam04997', 'pfam00562', 'pfam05000', 'pfam00623', 'pfam01191', 'pfam04561', 'TIGR02389']), set(['pfam00831', 'pfam01868', 'pfam00189', 'pfam00237']), set(['pfam01280', 'pfam00861', 'pfam01655']), set(['pfam01194', 'pfam00380', 'pfam00572']), set(['TIGR00425', 'pfam08068']), set(['pfam01157', 'pfam03874']), set(['pfam00416', 'TIGR01018']), set(['pfam00679', 'pfam03764']), set(['TIGR00344', 'TIGR03683']), set(['pfam01193', 'pfam01000']), set(['pfam00750', 'pfam05746']), set(['pfam00935', 'pfam01667']), set(['pfam00867', 'pfam00752']), set(['pfam01172', 'pfam09377']), set(['pfam03950', 'pfam00749']), set(['pfam00181', 'pfam03947']), set(['pfam00687', 'pfam00466']), set(['TIGR03679', 'TIGR00289']), set(['pfam01198', 'pfam01912']), set(['pfam00673', 'pfam00281']), set(['TIGR00134']), set(['pfam00410']), set(['pfam00411']), set(['pfam01090']), set(['pfam01092']), set(['pfam04919']), set(['TIGR00336']), set(['pfam01864']), set(['TIGR00442']), set(['pfam01866']), set(['pfam01780']), set(['TIGR01046']), set(['pfam00318']), set(['pfam00252']), set(['pfam09173']), set(['pfam00238']), set(['pfam01798']), set(['pfam01246']), set(['pfam07541']), set(['pfam00736']), set(['TIGR00522']), set(['pfam01269']), set(['TIGR00329']), set(['pfam01015']), set(['TIGR00392']), set(['pfam00203']), set(['TIGR00398']), set(['pfam01725']), set(['pfam02005']), set(['TIGR00422']), set(['pfam03439']), set(['pfam01351']), set(['pfam01922']), set(['pfam11987']), set(['pfam04127']), set(['TIGR00064']), set(['TIGR00389']), set(['pfam13656']), set(['pfam00298']), set(['TIGR00432']), set(['TIGR03677']), set(['pfam00958']), set(['pfam05221']), set(['pfam00347']), set(['TIGR03685']), set(['pfam03876']), set(['pfam01192']), set(['pfam01984']), set(['pfam00827']), set(['pfam01982']), set(['pfam01981']), set(['TIGR00408']), set(['TIGR00270']), set(['TIGR03665']), set(['pfam02978']), set(['pfam03484']), set(['pfam01201']), set(['TIGR02076']), set(['pfam00832']), set(['pfam00833']), set(['TIGR00419']), set(['pfam00177']), set(['pfam06418']), set(['TIGR00057']), set(['TIGR00549']), set(['pfam13685']), set(['pfam05670']), set(['pfam01849']), set(['TIGR02338']), set(['TIGR00468']), set(['pfam09249']), set(['pfam01287']), set(['pfam00164']), set(['pfam01282']), set(['TIGR03724']), set(['pfam01200']), set(['TIGR02153']), set(['TIGR00670']), set(['pfam00398']), set(['TIGR01213']), set(['pfam06026']), set(['pfam04019']), set(['pfam04010']), set(['pfam00366'])]")
print len(test)
for ms in markerSet.markerSet:
bMatch = False
for tms in test:
if tms == ms:
print ms
print tms
print '---------'
bMatch = True
break
if not bMatch:
print 'BOO!'
if str(markerSet.markerSet) == "[set(['TIGR01080', 'pfam08071', 'pfam00900']), set(['pfam08069', 'pfam00312']), set(['pfam00276', 'pfam00573', 'pfam00297']), set(['pfam00333', 'pfam00327', 'pfam03719']), set(['pfam04563', 'pfam04560', 'pfam04983', 'pfam04566', 'pfam04567', 'pfam04565', 'pfam04997', 'pfam00562', 'pfam05000', 'pfam00623', 'pfam01191', 'pfam04561', 'TIGR02389']), set(['pfam00831', 'pfam01868', 'pfam00189', 'pfam00237']), set(['pfam01280', 'pfam00861', 'pfam01655']), set(['pfam01194', 'pfam00380', 'pfam00572']), set(['TIGR00425', 'pfam08068']), set(['pfam01157', 'pfam03874']), set(['pfam00416', 'TIGR01018']), set(['pfam00679', 'pfam03764']), set(['TIGR00344', 'TIGR03683']), set(['pfam01193', 'pfam01000']), set(['pfam00750', 'pfam05746']), set(['pfam00935', 'pfam01667']), set(['pfam00867', 'pfam00752']), set(['pfam01172', 'pfam09377']), set(['pfam03950', 'pfam00749']), set(['pfam00181', 'pfam03947']), set(['pfam00687', 'pfam00466']), set(['TIGR03679', 'TIGR00289']), set(['pfam01198', 'pfam01912']), set(['pfam00673', 'pfam00281']), set(['TIGR00134']), set(['pfam00410']), set(['pfam00411']), set(['pfam01090']), set(['pfam01092']), set(['pfam04919']), set(['TIGR00336']), set(['pfam01864']), set(['TIGR00442']), set(['pfam01866']), set(['pfam01780']), set(['TIGR01046']), set(['pfam00318']), set(['pfam00252']), set(['pfam09173']), set(['pfam00238']), set(['pfam01798']), set(['pfam01246']), set(['pfam07541']), set(['pfam00736']), set(['TIGR00522']), set(['pfam01269']), set(['TIGR00329']), set(['pfam01015']), set(['TIGR00392']), set(['pfam00203']), set(['TIGR00398']), set(['pfam01725']), set(['pfam02005']), set(['TIGR00422']), set(['pfam03439']), set(['pfam01351']), set(['pfam01922']), set(['pfam11987']), set(['pfam04127']), set(['TIGR00064']), set(['TIGR00389']), set(['pfam13656']), set(['pfam00298']), set(['TIGR00432']), set(['TIGR03677']), set(['pfam00958']), set(['pfam05221']), set(['pfam00347']), set(['TIGR03685']), set(['pfam03876']), set(['pfam01192']), set(['pfam01984']), set(['pfam00827']), set(['pfam01982']), set(['pfam01981']), set(['TIGR00408']), set(['TIGR00270']), set(['TIGR03665']), set(['pfam02978']), set(['pfam03484']), set(['pfam01201']), set(['TIGR02076']), set(['pfam00832']), set(['pfam00833']), set(['TIGR00419']), set(['pfam00177']), set(['pfam06418']), set(['TIGR00057']), set(['TIGR00549']), set(['pfam13685']), set(['pfam05670']), set(['pfam01849']), set(['TIGR02338']), set(['TIGR00468']), set(['pfam09249']), set(['pfam01287']), set(['pfam00164']), set(['pfam01282']), set(['TIGR03724']), set(['pfam01200']), set(['TIGR02153']), set(['TIGR00670']), set(['pfam00398']), set(['TIGR01213']), set(['pfam06026']), set(['pfam04019']), set(['pfam04010']), set(['pfam00366'])]":
print 'Good to go!'
else:
print 'oh, shit!!!!'
