def kstring(string,dic):
""" splits and stores the strings coming from the classes file """
kname = ''
cmname = []
types = []
lines = string.strip().split('\n')
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'UNIQUE-ID':
kname = line[1]
if line[0] == 'COMMON-NAME':
cmname.append(line[1])
if line[0] == 'TYPES':
types.append(line[1])
k = dic.ksearch(kname)
if k == None:
k = EC.Class(kname)
dic.appendk(k)
for tname in types:
t = dic.ksearch(tname)
if t == None:
t = EC.Class(tname)
dic.appendk(t)
t.addchild(k)
k.addfather(t)
k.setcommname(cmname)
def qstring(string,dic):
""" splits and stores the strings coming from the proteins file """
name = ''
commname = []
types = []
comp = []
compof = []
reg = []
enz = []
lines = string.strip().split('\n')
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'UNIQUE-ID':
name = line[1]
elif line[0] == 'COMMON-NAME':
commname.append(line[1])
elif line[0] == 'TYPES':
k = dic.ksearch(line[1])
if k == None:
k = EC.Class(line[1])
dic.appendk(k)
types.append(k)
elif line[0] == 'COMPONENTS':
comp.append(line[1])
elif line[0] == '^COEFFICIENT':
for i in range(int(line[1])-1):
comp.append(comp[len(comp)-1])
elif line[0] == 'REGULATES':
reg.append(line[1])
elif line[0] == 'COMPONENT-OF':
compof.append(line[1])
elif line[0] == 'CATALYZES':
enz.append(line[1])
if name == '' or types == []:
print('- missing information for compound '+name+'\n')
if dic.qsearch(name) == None:
q = EC.Protein(name, commname, types, comp, compof, reg, enz)
dic.appendq(q)
else:
#error: compound already present
print('- protein '+name+' already existing in database at position'+str(dic.qsearch(name))+'\n')
for k in q.typ:
k.addg(q)
def cstring(string,dic):
""" splits and stores the strings coming from the compounds file """
name = ''
commname = []
types = []
reglst = []
smiles = ''
weight = 0
lines = string.strip().split('\n')
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'UNIQUE-ID':
name = line[1]
if line[0] == 'COMMON-NAME':
commname.append(line[1])
if line[0] == 'TYPES':
k = dic.ksearch(line[1])
if k == None:
k = EC.Class(line[1])
dic.appendk(k)
types.append(k)
if line[0] == 'SMILES':
smiles = line[1]
if line[0] == 'WEIGHT':
weight = int(line[1])
if line[0] == 'REGULATES':
reglst.append(line[1])
if name == '' or types == [] or smiles == '':
print('- missing information for compound '+name+'\n')
if dic.csearch(name) == None:
c = EC.Compound(name, commname, types, smiles, weight, reglst)
dic.appendc(c)
else:
#error: compound already present
print('- compound '+name+' already existing in database at position'+str(dic.csearch(name))+'\nThe input is:\n'+string)
for k in c.typ:
k.addg(c)
def ExportGraphs(dic,organism): for p1 in dic.plst: if p1.name in ['GLYCOLYSIS-E-D', 'GLYCOLYSIS', 'GLYCOLYSIS-TCA-GLYOX-BYPASS']: totgraphname = './results/'+organism+'/'+p1.name+'_tot.gml' primgraphname = './results/'+organism+'/'+p1.name+'_prim.gml' GO.write_pathway_gml(p1.totgraph,p1.elst,totgraphname) p1.primgraph.write_gml(primgraphname) for p2 in dic.plst: if p2.name in ['GLUCONEO-PWY','FERMENTATION-PWY','HEXITOLDEGSUPER-PWY','FAO-PWY','PWY0-1337','PENTOSE-P-PWY','TREDEGLOW-PWY']: mergedname = './results/'+organism+'/graphs/'+p1.name+'+'+p2.name+'_tot.gml' GO.write_pathway_gml(EC.merge(p1.totgraph,p2.totgraph),list(set(p1.elst[:]+p2.elst[:])),mergedname)
def mstring(line,colors,dic):
"""
calculates all the possible color configurations on the edges contained in line,
creates the corresponding object and stores them as motifs in the dic attribute mlst.
"""
lst = line.strip().split(' ')
elst = [(int(lst[i]),int(lst[i+1])) for i in range(2,len(lst),2)]
g = Graph(int(lst[0]),directed=True)
g.vs['name'] = range(len(g.vs[:]))
g.add_edges(elst)
clst = colorlst(elst,colors)
for c in clst:
print c
g.es['color'] = c
m = EC.Motif(g.copy())
dic.appendm(m)
def ExportGraphs(dic, organism):
for p1 in dic.plst:
if p1.name in [
'GLYCOLYSIS-E-D', 'GLYCOLYSIS', 'GLYCOLYSIS-TCA-GLYOX-BYPASS'
]:
totgraphname = './results/' + organism + '/' + p1.name + '_tot.gml'
primgraphname = './results/' + organism + '/' + p1.name + '_prim.gml'
GO.write_pathway_gml(p1.totgraph, p1.elst, totgraphname)
p1.primgraph.write_gml(primgraphname)
for p2 in dic.plst:
if p2.name in [
'GLUCONEO-PWY', 'FERMENTATION-PWY',
'HEXITOLDEGSUPER-PWY', 'FAO-PWY', 'PWY0-1337',
'PENTOSE-P-PWY', 'TREDEGLOW-PWY'
]:
mergedname = './results/' + organism + '/graphs/' + p1.name + '+' + p2.name + '_tot.gml'
GO.write_pathway_gml(EC.merge(p1.totgraph, p2.totgraph),
list(set(p1.elst[:] + p2.elst[:])),
mergedname)
def pstring(temp, firstiteration, dic):
""" splits and stores the strings coming from the pathways file """
#rctlst = ''
lines = temp.split('\n')
for i in lines:
l = i.strip().split(' - ')
if l[0] == 'UNIQUE-ID':
name = l[1]
p = dic.psearch(name)
if p == None:
p = EC.Pathway(name)
dic.appendp(p)
if p.finished == True:
return True
if l[0] == 'COMMON-NAME' and p.commname == '':
p.commname = l[1]
if l[0] == 'REACTION-LAYOUT':
inel = []
outel = []
rct = re.search('\((.*) \(:LEFT-PRIMARIES(.*)\) \(:DIRECTION (.*)\) \(:RIGHT-PRIMARIES(.*)\)\)',l[1])
if rct.group(2)=='' and rct.group(4)=='':
subpname = rct.group(1)
subp = dic.psearch(subpname)
if subp == None:
subp = EC.Pathway(subpname)
dic.appendp(subp)
if firstiteration:
p.todo.append(subp)
p.splst.append(subp)
elif subp.finished == True and subp in p.todo:
for i in range(len(subp.rlst)):
p.appendr(subp.rlst[i],subp.primlst[i])
p.todo.remove(subp)
if len(p.todo) == 0:
#the last subp has just been added: declare the path as finished and
#add the pathway to all the plst of all compounds and to reactions involved
p.finished = True
else:
continue
elif firstiteration and rct.group(3) == ':L2R':
inel = dic.glst([i.strip('|') for i in rct.group(2).strip().split(' ')])
outel = dic.glst([i.strip('|') for i in rct.group(4).strip().split(' ')])
r = dic.rsearch(rct.group(1).strip('|'))
if r == None:
print('Fatal error during decoding of pathway '+p.name+': the reaction '+rct.group(1)+' has not been found in the database')
p.appendr(r,(inel,outel))
appinpath(inel,p)
appinpath(outel,p)
elif firstiteration and rct.group(3) == ':R2L':
inel = dic.glst([i.strip('|') for i in rct.group(4).strip().split(' ')])
outel = dic.glst([i.strip('|') for i in rct.group(2).strip().split(' ')])
r = dic.rsearch(rct.group(1).strip('|'))
if r == None:
print('Fatal error during decoding of pathway '+p.name+': the reaction '+rct.group(1)+' has not been found in the database')
p.appendr(r,(inel,outel))
appinpath(inel,p)
appinpath(outel,p)
elif firstiteration:
print 'broken pathway: '
print temp
p.todo = []
if len(p.todo) == 0:
p.finished = True
return True
else:
return False
def estring(string,dic):
""" splits and stores the strings coming from the regulation file """
name = ''
commname = ''
regulator = ''
renzname = ''
mechanism = 'x'
activation = None
found = False
cs = []
rct = None
lines = string.strip().split('\n')
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'TYPES':
if line[1] == 'Regulation-of-Enzyme-Activity':
found = True
break
if found == True:
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'REGULATED-ENTITY':
renzname = line[1]
rct = dic.renzsearch(renzname)
found = False
if found == True:
return None
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'UNIQUE-ID':
name = line[1]
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'COMMON-NAME':
commname = line[1]
if line[0] == 'MECHANISM' and mechanism == 'x':
if line[1] == 'COMPETITIVE':
mechanism = 'c'
elif line[1] == 'ALLOSTERIC':
mechanism = 'a'
else:
mechanism = 'n'
if line[0] == 'MODE' and activation == None:
if line[1] == '-':
activation = False
elif line[1] == '+':
activation = True
else:
activation = None
if line[0] == 'REGULATOR' and regulator == '':
g = dic.gsearch(line[1])
cs.append(g)
if g == None:
return None
e = EC.Regulation(name, commname, cs, mechanism, activation, rct)
rct.elst.append(e)
dic.appende(e)
def rstring(string,dic):
""" splits and stores the strings coming from the reactions file """
rname = ''
typ = []
commname = []
enames = []
innames = []
outnames = []
slst = []
tlst = []
nobalance = False
inpath = []
reversible = True
lines = string.strip().split('\n')
reverse = False
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'UNIQUE-ID':
rname = line[1]
if line[0] == 'REACTION-DIRECTION':
reverse = False
if re.search('LEFT-TO-RIGHT',line[1]):
reversible = False
if re.search('RIGHT-TO-LEFT',line[1]):
reversible = False
reverse = True
if line[0] == 'ENZYMATIC-REACTION':
enames.append(line[1])
if line[0] == 'SYNONYMS':
commname.append(line[1])
if line[0] == 'TYPES':
typ.append(line[1])
if line[0] == 'IN-PATHWAY':
inpath.append(line[1])
if line[0] == 'CANNOT-BALANCE?' and line[1] in ['T','NIL']:
nobalance = True
if reverse == False:
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'LEFT':
innames.append(line[1].strip('|'))
slst.append(1)
tlst.append('CCO-IN')
if line[0] == 'RIGHT':
outnames.append(line[1].strip('|'))
slst.append(-1)
tlst.append('CCO-IN')
if line[0] == '^COEFFICIENT':
if 'n' in line[1]:
line[1] = '0'
if 'x' in line[1]:
line[1] = '1'
slst[len(slst)-1] = slst[len(slst)-1]*int(line[1])
if line[0] == '^COMPARTMENT':
tlst[len(tlst)-1] = line[1]
if reverse == True:
for i in lines:
line = i.strip().split(' - ')
if line[0] == 'RIGHT':
innames.append(line[1].strip('|'))
slst.append(1)
tlst.append('CCO-IN')
if line[0] == 'LEFT':
outnames.append(line[1].strip('|'))
slst.append(-1)
tlst.append('CCO-IN')
if line[0] == '^COEFFICIENT':
if 'n' in line[1]:
line[1] = '0'
if 'x' in line[1]:
line[1] = '1'
slst[len(slst)-1] = slst[len(slst)-1]*int(line[1])
if line[0] == '^COMPARTMENT':
tlst[len(tlst)-1] = line[1]
r = EC.Reaction([rname, commname, typ, innames, outnames, slst, tlst, nobalance, reversible, enames, inpath, dic])
dic.appendr(r)
elif renzname not in e.rct.ename:
print('Registration error for '+e.name+':\t\t'+str(e.rct.ename)+' -- '+renzname)
#interface
#add functions
#create graph
if __name__ == "__main__":
organism = raw_input('Organism? (ecoli/yeast[custom]) \n')
if organism == '':
organism = 'yeast'
dic = EC.ReactDic(organism)
decode(organism,dic)
with open('./results/logmeta.log','w') as out1:
for r in dic.rlst:
if len(r.elst) >= 2:
out1.write('\n'+r.name+'\n')
for e in r.elst:
out1.write(str(e.activation)+'\t'+e.cs[0].name+'\n')
ppcorrp = [0] * (len(dic.plst)*len(dic.plst))
ppcorrn = [0] * (len(dic.plst)*len(dic.plst))
for e in dic.elst:
cs = e.cs[0]
r = e.rct
if e.activation == None:
continue