def __init__(self, name):
super().__init__(name, type='CompCOB')
if self.cob:
self.cob = COB(self.cob)
if self.ont:
self.ont = Ontology(self.ont)
try:
# Open the HDF5 store
self.hdf5 = self._hdf5(name)
self.densities = self.hdf5['densities']
except KeyError:
self.densities = DataFrame()
class CompCOB(Camoco):
def __init__(self, name):
super().__init__(name, type='CompCOB')
if self.cob:
self.cob = COB(self.cob)
if self.ont:
self.ont = Ontology(self.ont)
try:
# Open the HDF5 store
self.hdf5 = self._hdf5(name)
self.densities = self.hdf5['densities']
except KeyError:
self.densities = DataFrame()
@classmethod
def compare(cls, cob, ont, name, description, min_members=3,
max_members=300, random_trials=100, sig_threshold=0.05,
debug=False):
self = super().create(name, description, type='CompCOB')
# Assign the COB and Ontology classes
self.cob = cob
self.ont = ont
# Save the arguments for later retreival
self._global('cob', cob.name)
self._global('ont', ont.name)
self._global('min_members', min_members)
self._global('max_members', max_members)
self._global('sig_threshold', sig_threshold)
self._global('random_trials', random_trials)
# Finding the terms and their genes
self.ont_loci = self._find_term_loci(
min_members=min_members, max_members=max_members
)
# Runnign the actual comparison
self.densities = self._run_comparison(
random_trials=random_trials,
sig_threshold=sig_threshold, debug=debug
)
# Save the results
self.log('Writing the results to the database.')
# self.hdf5['ont_loci'] = DataFrame(self.ont_loci.items())
self.hdf5['densities'] = self.densities
return self
def _find_term_loci(self, min_members=3, max_members=300):
self.log('Finding the ontology terms.')
ont_list = self.ont.terms()
ont_loci = dict()
self.log('Found {} total terms in the onotlogy.', len(ont_list))
self.log('Filtering the terms and finding their genes.')
count = 0
for term in ont_list:
# Filtering out the terms with too few or too many genes
filt_loci = [x for x in term.locus_list if x in self.cob]
if len(filt_loci) >= min_members and len(filt_loci) <= max_members:
ont_loci[term.id] = filt_loci
count += 1
self.log('Found {} terms elegible for analysis.', count)
return ont_loci
def _run_comparison(self, random_trials=100,
sig_threshold=0.05, debug=False):
self.log(
'Running ' + str(random_trials) +
' random sets for each term and comparing them.')
dens = dict()
significant_terms = 0
n = 0
# Use only 25 terms for testing purposes
if debug:
ont_loci = list(self.ont_loci.items())[:25]
else:
ont_loci = list(self.ont_loci.items())
# Iterate through all terms
for term, loci in ont_loci:
# Log how many teerms are done, to ensure people it hasn't crashed
if n % 100 == 0:
self.log('Compared {}/{} terms so far.', n, len(ont_loci))
real_density = self.cob.density(loci)
dens[term] = [real_density]
# Run the random samples
loci_count = len(loci)
loci_tot_list = self.cob.refgen.random_genes(
loci_count*random_trials
)
scores = []
aboves = 0
for x in range(random_trials):
# Get the random genes
loci_list = [loci_tot_list.pop() for x in range(loci_count)]
# Find the density and save it
score = self.cob.density(loci_list)
if score >= real_density:
aboves += 1
scores.append(score)
# Add on the states from the scores
dens[term].append(np.mean(scores))
dens[term].append(np.std(scores))
dens[term].append(aboves)
# Figure out if that makes it significant
if dens[term][-1] <= (random_trials*sig_threshold):
dens[term].append(1)
significant_terms += 1
else:
dens[term].append(0)
n += 1
self.log('Compared all {} terms.', n)
# Convert the dict to a DataFrame
ans = DataFrame.from_items(
dens.items(),
columns=[
self.cob.name+' Density', 'Random Density Mean',
'Random STD', 'Items >= '+self.cob.name, 'Significant'
],
orient='index'
)
self.log('Number of Significant Terms: ' + str(significant_terms))
self.log('Number Random Significants Expected: '+str(len(dens)*0.05))
return ans
def to_cytoscape(self,obo_file,out_file):
self.log('Importing OBO: {}',obo_file)
terms = defaultdict(dict)
cur_term = ''
alt_terms = []
alts = set()
isa_re = re.compile('is_a: (.*) !.*')
with open(obo_file,'r') as INOBO:
for line in INOBO:
line = line.strip()
if line.startswith('id: '):
for alt in alt_terms:
terms[alt] = terms[cur_term].copy()
alt_terms = []
cur_term = line.replace('id: ','')
elif line.startswith('name: '):
terms[cur_term]['name'] = line.replace('name: ','')
terms[cur_term]['desc'] = ''
terms[cur_term]['is_a'] = []
terms[cur_term]['genes'] = set()
elif line.startswith('namespace: '):
terms[cur_term]['type'] = line.replace('namespace: ','')
elif line.startswith('alt_id: '):
alt_terms.append(line.replace('alt_id: ',''))
alts.add(line.replace('alt_id: ',''))
elif line.startswith('def: '):
terms[cur_term]['desc'] += line.replace('def: ','')
elif line.startswith('comment: '):
terms[cur_term]['desc'] += line.replace('comment: ','')
elif line.startswith('is_a: '):
terms[cur_term]['is_a'].append(isa_re.match(line).group(1))
def getISA(terms,term,alts):
rels = []
if terms[term]['is_a'] == []:
return None
else:
for isa in terms[term]['is_a']:
if isa not in alts:
rels.append((term,isa))
for isa in terms[term]['is_a']:
if isa not in alts:
x = getISA(terms,isa,alts)
if x:
rels += x
return rels
self.log('Adding the edges.')
graph = nx.DiGraph()
for term in self.densities.index:
if term not in alts:
x = getISA(terms,term,alts)
if x:
graph.add_edges_from(x)
self.log('Adding the node information.')
all_nodes = set(list(graph.nodes()) + list(self.densities.index))
for id in all_nodes:
if id not in alts:
if id in self.densities.index:
sig = int(self.densities['Significant'][id])
else:
sig = 0
graph.add_node(id, significant=sig, name=terms[id]['name'], desc=terms[id]['desc'])
self.log('Done.')
nx.write_graphml(graph,out_file)
return graph
def report(self, folder=''):
# Figuring out the names for everything
zipname = os.path.join(folder, self.cob.name+'EvalReport.zip')
rawname = os.path.join(folder, self.cob.name+'RawEval.csv')
termsname = os.path.join(folder, 'sigTerms.txt')
readmename = os.path.join(folder, 'EvalREADME.txt')
self.log('Writing the raw data.')
self.densities.to_csv(path_or_buf=rawname)
self.log('Writing the significant terms.')
terms = self.densities[self.densities['Significant'] > 0]
termsfile = open(termsname, 'w')
for term in list(terms.index):
termsfile.write(str(self.ont[term])+'\n')
termsfile.close()
self.log('Writing the README.')
readme = open(readmename, 'w')
readme.write((
'This contains two files that were made from doing a comparison '
'of density in the COB network based on GO terms vs. random '
'trials. The method was just finding all of the terms that are in the'
' GO ontology that are anotated for maize, giving the list of genes to'
' the density function in the COB class and getting that back.'
' Then we picked the same ammount of random genes that are in the term'
' and did the density measurement. After repeating this 100 times,'
' we count how many densities are bigger than the real network, if'
' it is less than 5, it is considered significant.'
'Contained are two files, the raw data and the list of terms '
'that were considered significant. Here are some other relevant '
'stats: Total Testable Terms: '+str(len(self.densities))+'\n'
'Total Significant Terms: '+str(len(terms))+'\n'
'The Expected Number of False Significants: '
+ str(len(self.densities)*0.05) + '\n'
'Let me know if you want any other stats or information, or '
'have suggestions as to what is or is not useful in a '
'report about a dataset.'
'Joe Jeffers'
'*****@*****.**'
))
readme.close()
self.log('Zipping it all up.')
os.system(
'zip -j -q '+zipname+' '+rawname+' '+termsname+' '+readmename
)
os.system('rm '+rawname+' '+termsname+' '+readmename)
self.log('Done, please check '+folder+' for your results.')
return