class EvalAdmix():
'Class for executing evalAdmix commands'
def __init__(self,prefix,mc,funcs):
self.prefix = prefix
self.mc = mc
self.mcOnly = False
if(self.mc != "none"):
self.mcOnly = True
self.qfiles = dict()
self.runs = dict()
self.qfilePaths = dict()
if(self.mcOnly == True):
self.parseMC()
#import R functions
self.utils = importr('utils')
self.base = importr('base')
self.grdevices = importr('grDevices')
# import R plotting functions from evalAdmix
with open(funcs, 'r') as f:
string = f.read()
self.myfunc = STAP(string, "myfunc")
def parseMC(self):
print("Parsing MC")
with open(self.mc) as fh:
newlist = fh.read().splitlines()
print(newlist)
def loadJson(self):
self.loadQ()
self.loadRuns()
self.loadQfilePaths()
def loadQ(self):
qfn = self.prefix + ".qfiles.json"
if os.path.isfile(qfn):
with open(qfn) as fh:
self.qfiles = json.load(fh)
else:
print("ERROR:", qfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def loadRuns(self):
rfn = "cvRuns.json"
if os.path.isfile(rfn):
with open(rfn) as fh:
self.runs = json.load(fh)
else:
print("ERROR:", rfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def loadQfilePaths(self):
rfn = "qfilePaths.json"
if os.path.isfile(rfn):
with open(rfn) as fh:
self.qfilePaths = json.load(fh)
else:
print("ERROR:", rfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def evalAdmix(self, minK, maxK, np):
ks = range(int(minK), int(maxK)+1)
for k in ks:
for qf in self.qfiles[str(k)]:
print(qf)
temp = qf.split(".")
#make .P file name
temp[-1] = "P"
pf = ".".join(temp)
#make output .corres file name
temp[-1] = "corres"
eAf = ".".join(temp)
#build command for evalAdmix
evalAdmix_str_com = "evalAdmix -plink " + self.prefix + " -fname " + pf + " -qname " + qf + " -o " + eAf + " -P " + str(np)
call = SysCall(evalAdmix_str_com)
call.run_program()
def averageCorres(self, funcs):
for k in self.runs:
matrixList = list()
print(k)
for run in self.runs[k]:
temp = run.split(".")
temp[-1] = "corres"
eAf = ".".join(temp)
if(os.path.isfile(eAf)):
cor = self.base.as_matrix(self.utils.read_table(eAf))
matrixList.append(cor)
else:
print("ERROR:", eAf, "does not exist.")
print("Exiting program...")
raise SystemExit
reducedList = self.base.Reduce('+', matrixList) #sum matrices in list
cor = reducedList.ro/float(len(matrixList)) #div by num elements in list to get mean
q = self.parseClumpp(self.qfilePaths[k])
famf = self.prefix + ".fam"
pop = self.base.as_matrix(self.utils.read_table(famf))
output = k + ".png"
ordr = self.myfunc.orderInds(pop=self.base.as_vector(pop.rx(True,2)), q=q)
title=k
self.grdevices.png(file=output)
try:
self.myfunc.plotCorRes(cor_mat=cor, pop=self.base.as_vector(pop.rx(True,2)), ord=ordr, title=title, max_z=0.1, min_z=-0.1)
except rpy2.rinterface_lib.embedded.RRuntimeError:
print("Error in R code (plotting functions) from evalAdmix.")
self.grdevices.dev_off()
def parseClumpp(self,f):
if(os.path.isfile(f)):
df = pandas.read_csv(f, delimiter="\s+", header=None, index_col=False)
df.drop(df.columns[0:5],axis=1,inplace=True)
#print(df)
with localconverter(rpy2.robjects.default_converter + pandas2ri.converter):
Rdf = rpy2.robjects.conversion.py2rpy(df)
#print(Rdf)
return Rdf
def Rcode(self, funcs, minK, maxK):
#make file names
famf = self.prefix + ".fam"
ks = range(int(minK), int(maxK)+1)
for k in ks:
title="K="+str(k)
for qf in self.qfiles[str(k)]:
temp = qf.split(".")
temp[-1] = "corres"
eAf = ".".join(temp)
output = eAf + ".png"
# read in files
pop = self.base.as_matrix(self.utils.read_table(famf))
print(qf)
q = self.utils.read_table(qf)
cor = self.base.as_matrix(self.utils.read_table(eAf))
# run plotting functions
ordr = self.myfunc.orderInds(pop=self.base.as_vector(pop.rx(True,2)), q=q)
self.grdevices.png(file=output)
try:
self.myfunc.plotCorRes(cor_mat=cor, pop=self.base.as_vector(pop.rx(True,2)), ord=ordr, title=title, max_z=0.1, min_z=-0.1)
except rpy2.rinterface_lib.embedded.RRuntimeError:
print("Something happened.")
self.grdevices.dev_off()
class EvalAdmix():
'Class for executing evalAdmix commands'
def __init__(self, prefix, mc, funcs):
self.prefix = prefix
self.mc = mc
self.mcOnly = False
if (self.mc != "none"):
self.mcOnly = True
self.qfiles = dict()
self.runs = dict()
self.qfilePaths = dict()
if (self.mcOnly == True):
self.parseMC()
#import R functions
self.utils = importr('utils')
self.base = importr('base')
self.grdevices = importr('grDevices')
# import R plotting functions from evalAdmix
with open(funcs, 'r') as f:
string = f.read()
self.myfunc = STAP(string, "myfunc")
def parseMC(self):
print("Parsing MC")
with open(self.mc) as fh:
newlist = fh.read().splitlines()
print(newlist)
def loadJson(self):
self.loadQ()
self.loadRuns()
self.loadQfilePaths()
def loadQ(self):
qfn = self.prefix + ".qfiles.json"
if os.path.isfile(qfn):
with open(qfn) as fh:
self.qfiles = json.load(fh)
else:
print("ERROR:", qfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def loadRuns(self):
rfn = "cvRuns.json"
if os.path.isfile(rfn):
with open(rfn) as fh:
self.runs = json.load(fh)
else:
print("ERROR:", rfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def loadQfilePaths(self):
rfn = "qfilePaths.json"
if os.path.isfile(rfn):
with open(rfn) as fh:
self.qfilePaths = json.load(fh)
else:
print("ERROR:", rfn, "does not exist.")
print("Exiting program...")
raise SystemExit
def evalAdmix(self, minK, maxK, np):
ks = range(int(minK), int(maxK) + 1)
for k in ks:
for qf in self.qfiles[str(k)]:
print(qf)
temp = qf.split(".")
#make .P file name
temp[-1] = "P"
pf = ".".join(temp)
#make output .corres file name
temp[-1] = "corres"
eAf = ".".join(temp)
#build command for evalAdmix
evalAdmix_str_com = "evalAdmix -plink " + self.prefix + " -fname " + pf + " -qname " + qf + " -o " + eAf + " -P " + str(
np)
call = SysCall(evalAdmix_str_com)
call.run_program()
def averageCorres(self, funcs):
for k in self.runs:
matrixList = list()
print(k)
for run in self.runs[k]:
temp = run.split(".")
temp[-1] = "corres"
eAf = ".".join(temp)
if (os.path.isfile(eAf)):
cor = self.base.as_matrix(self.utils.read_table(eAf))
matrixList.append(cor)
else:
print("ERROR:", eAf, "does not exist.")
print("Exiting program...")
raise SystemExit
reducedList = self.base.Reduce('+',
matrixList) #sum matrices in list
cor = reducedList.ro / float(
len(matrixList)) #div by num elements in list to get mean
#get average corres matrix for major or minor cluster k
q = self.parseClumpp(self.qfilePaths[k])
#check if object q is NoneType
if q is None:
print("")
print("")
print("ERROR from evaladmix.py:")
print(
"Empty matrices (Python NoneType) were returned When trying to create average matrices for Major/Minor clusters."
)
print("Check that the paths in qfilePaths.json are valid.")
print(
"This error could occur if you have moved your admixture run folder after running distructRerun.py."
)
print(
"Alternatively, if you are using the Docker container this could have occurred if you ran distructRerun.py on your own system outside of the container."
)
print("")
print("")
raise SystemExit
famf = self.prefix + ".fam"
pop = self.base.as_matrix(self.utils.read_table(famf))
# uncomment lines below for debugging of object types
#print("Type for q is:")
#print(type(q))
# uncomment below lines for debugging.
#print(type(pop))
#print(type(famf))
output = k + ".png"
ordr = self.myfunc.orderInds(pop=self.base.as_vector(
pop.rx(True, 2)),
q=q)
title = k
self.grdevices.png(file=output)
try:
self.myfunc.plotCorRes(cor_mat=cor,
pop=self.base.as_vector(pop.rx(True,
2)),
ord=ordr,
title=title,
max_z=0.1,
min_z=-0.1)
except rpy2.rinterface_lib.embedded.RRuntimeError:
print("Error in R code (plotting functions) from evalAdmix.")
self.grdevices.dev_off()
def parseClumpp(self, f):
if (os.path.isfile(f)):
df = pandas.read_csv(f,
delimiter="\s+",
header=None,
index_col=False)
# Even though inplace=True is used in this context, operating on the dataframe directly rather than assigning to a new variable should prevent creation of a "NoneType"
df.drop(df.columns[0:5], axis=1, inplace=True)
# uncomment below lines for debugging.
#print("Type for df is:")
#print(type(df))
with localconverter(rpy2.robjects.default_converter +
pandas2ri.converter):
Rdf = rpy2.robjects.conversion.py2rpy(df)
# uncomment lines below for debugging.
#print("Type for Rdf is:")
#print(type(Rdf))
#print(Rdf)
return Rdf
def Rcode(self, funcs, minK, maxK):
#make file names
famf = self.prefix + ".fam"
ks = range(int(minK), int(maxK) + 1)
for k in ks:
title = "K=" + str(k)
for qf in self.qfiles[str(k)]:
temp = qf.split(".")
temp[-1] = "corres"
eAf = ".".join(temp)
output = eAf + ".png"
# read in files
pop = self.base.as_matrix(self.utils.read_table(famf))
print(qf)
q = self.utils.read_table(qf)
cor = self.base.as_matrix(self.utils.read_table(eAf))
# run plotting functions
ordr = self.myfunc.orderInds(pop=self.base.as_vector(
pop.rx(True, 2)),
q=q)
self.grdevices.png(file=output)
try:
self.myfunc.plotCorRes(cor_mat=cor,
pop=self.base.as_vector(
pop.rx(True, 2)),
ord=ordr,
title=title,
max_z=0.1,
min_z=-0.1)
except rpy2.rinterface_lib.embedded.RRuntimeError:
print("Something happened.")
self.grdevices.dev_off()
