def test_one(self):
logging.info("TestEpistasis test_one")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase, count_A1=False)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one")
frame = epistasis(
test_snps,
pheno,
G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file,
count_A1=False)
sid0, sid1, pvalue_list = np.array(frame['SNP0']), np.array(
frame['SNP1']), np.array(frame['PValue'])
#Check the output file
self.compare_files(sid0, sid1, pvalue_list, "one")
#Check the values returned
output_file2 = self.file_name("one_again")
write(sid0, sid1, pvalue_list, output_file2)
self.compare_files(sid0, sid1, pvalue_list, "one")
def test_unknown_sid(self):
logging.info("TestEpistasis test_unknown_sid")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
try:
frame = epistasis(test_snps, pheno,covar=covar,sid_list_0=['1_4','bogus sid','1_9'],sid_list_1=test_snps.sid[5:15]) #Skip 5 snps, use next 10
failed = False
except:
failed = True
assert(failed)
def test_no_cov(self):
logging.info("TestEpistasis test_no_cov")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
output_file = self.file_name("no_cov")
frame = epistasis(test_snps, pheno, G0=test_snps,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"no_cov")
def test_no_sid_list_0(self):
logging.info("TestEpistasis test_no_sid_list_0")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("no_sid_list_0")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=['1_4'],
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"no_sid_list_0")
def test_preload_files(self):
logging.info("TestEpistasis test_preload_files")
from pysnptools.snpreader import Bed
test_snps = self.bedbase
pheno = pstpheno.loadOnePhen(self.phen_fn,vectorize=True)
covar = pstpheno.loadPhen(self.cov_fn)
bed = Bed(test_snps)
output_file = self.file_name("preload_files")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=bed.sid[:10], #first 10 snps
sid_list_1=bed.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"one")
def test_no_cov_b(self):
logging.info("TestEpistasis test_no_cov_b")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
output_file = self.file_name("no_cov_b")
covar = pstpheno.loadPhen(self.cov_fn)
covar['vals'] = np.delete(covar['vals'], np.s_[:],1) #Remove all the columns
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"no_cov")
def test_G1_mixing(self):
logging.info("TestEpistasis test_G1_mixing")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase,count_A1=False)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("G1_mixing")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
G1=test_snps,
mixing=0,
output_file_name=output_file,count_A1=False
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"one")
def test_G1_mixing(self):
logging.info("TestEpistasis test_G1_mixing")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase,count_A1=False)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("G1_mixing")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
G1=test_snps,
mixing=0,
output_file_name=output_file,count_A1=False
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"one")
def test_cid_intersect(self):
logging.info("TestEpistasis test_cid_intersect")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = pstpheno.loadOnePhen(self.phen_fn,vectorize=True)
pheno['iid'] = np.vstack([pheno['iid'][::-1],[['Bogus','Bogus']]])
pheno['vals'] = np.hstack([pheno['vals'][::-1],[-34343]])
covar = self.cov_fn
output_file = self.file_name("cid_intersect")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
self.compare_files(sid0,sid1,pvalue_list,"one")
def test_match_cpp(self):
'''
match
FaSTLMM.207\Data\DemoData>fastlmmc -snpPairs -bfile snps -extract topsnps.txt -bfileSim snps -extractSim ASout.snps.txt -pheno pheno.txt -covar covariate.txt -out topsnps.pairs.txt -logDelta 0 -verbose 100
'''
logging.info("TestEpistasis test_match_cpp")
from pysnptools.snpreader import Bed
snps = Bed(os.path.join(self.pythonpath, "tests/datasets/selecttest/snps"))
pheno = os.path.join(self.pythonpath, "tests/datasets/selecttest/pheno.txt")
covar = os.path.join(self.pythonpath, "tests/datasets/selecttest/covariate.txt")
sim_sid = ["snp26250_m0_.19m1_.19","snp82500_m0_.28m1_.28","snp63751_m0_.23m1_.23","snp48753_m0_.4m1_.4","snp45001_m0_.26m1_.26","snp52500_m0_.05m1_.05","snp75002_m0_.39m1_.39","snp41253_m0_.07m1_.07","snp11253_m0_.2m1_.2","snp86250_m0_.33m1_.33","snp3753_m0_.23m1_.23","snp75003_m0_.32m1_.32","snp30002_m0_.25m1_.25","snp26252_m0_.19m1_.19","snp67501_m0_.15m1_.15","snp63750_m0_.28m1_.28","snp30001_m0_.28m1_.28","snp52502_m0_.35m1_.35","snp33752_m0_.31m1_.31","snp37503_m0_.37m1_.37","snp15002_m0_.11m1_.11","snp3751_m0_.34m1_.34","snp7502_m0_.18m1_.18","snp52503_m0_.3m1_.3","snp30000_m0_.39m1_.39","isnp4457_m0_.11m1_.11","isnp23145_m0_.2m1_.2","snp60001_m0_.39m1_.39","snp33753_m0_.16m1_.16","isnp60813_m0_.2m1_.2","snp82502_m0_.34m1_.34","snp11252_m0_.13m1_.13"]
sim_idx = snps.sid_to_index(sim_sid)
test_sid = ["snp26250_m0_.19m1_.19","snp63751_m0_.23m1_.23","snp82500_m0_.28m1_.28","snp48753_m0_.4m1_.4","snp45001_m0_.26m1_.26","snp52500_m0_.05m1_.05","snp75002_m0_.39m1_.39","snp41253_m0_.07m1_.07","snp86250_m0_.33m1_.33","snp15002_m0_.11m1_.11","snp33752_m0_.31m1_.31","snp26252_m0_.19m1_.19","snp30001_m0_.28m1_.28","snp11253_m0_.2m1_.2","snp67501_m0_.15m1_.15","snp3753_m0_.23m1_.23","snp52502_m0_.35m1_.35","snp30000_m0_.39m1_.39","snp30002_m0_.25m1_.25"]
test_idx = snps.sid_to_index(test_sid)
frame = epistasis(snps[:,test_idx], pheno,covar=covar, G0 = snps[:,sim_idx],log_delta=0)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
referenceOutfile = TestFeatureSelection.reference_file("epistasis/topsnps.pairs.txt")
import pandas as pd
table = pd.read_table(referenceOutfile,sep="\t") # We've manually remove all comments and blank lines from this file
assert len(pvalue_list) == len(table)
for row in table.iterrows():
snp0cpp,snp1cpp,pvaluecpp,i1,i2 = row[1]
for i in xrange(len(pvalue_list)):
found = False
pvaluepy = pvalue_list[i]
snp0py = sid0[i]
snp1py = sid1[i]
if (snp0py == snp0cpp and snp1py == snp1cpp) or (snp0py == snp1cpp and snp1py == snp0cpp):
found = True
diff = abs(pvaluecpp - pvaluepy)/pvaluecpp
assert diff < .035, "'{0}' '{1}' pvalue_list differ too much {4} -- {2} vs {3}".format(snp0cpp,snp1cpp,pvaluecpp,pvaluepy,diff)
break
assert found
def test_one(self):
logging.info("TestEpistasis test_one")
from pysnptools.snpreader import Bed
test_snps = Bed(self.bedbase)
pheno = self.phen_fn
covar = self.cov_fn
output_file = self.file_name("one")
frame = epistasis(test_snps, pheno, G0=test_snps,
covar=covar,
sid_list_0=test_snps.sid[:10], #first 10 snps
sid_list_1=test_snps.sid[5:15], #Skip 5 snps, use next 10
output_file_name=output_file
)
sid0,sid1,pvalue_list =np.array(frame['SNP0']),np.array(frame['SNP1']),np.array(frame['PValue'])
#Check the output file
self.compare_files(sid0,sid1,pvalue_list,"one")
#Check the values returned
output_file2 = self.file_name("one_again")
write(sid0,sid1,pvalue_list,output_file2)
self.compare_files(sid0,sid1,pvalue_list,"one")
def run_fastlmmc(dataset, output_dir, process_id, group_size, covFile=None, species='mouse', maxthreads=1, featsel=False, exclude=False, condition=None):
# commands from fastlmmc:
# maxthreads
# condition
# exclude by position
# if condition:
# condition = '-SnpId1 %s' % condition[0]
# else:
# condition = '
bfile = dataset
filtered_snp_reader = Bed('%s.FILTERED' % bfile)
full_snp_reader = Bed('%s.FULL' % bfile)
pheno = '%s.pheno.txt' % dataset
v = globals()
chroms = map(str, range(1, species_chroms[species] + 1))
v.update(locals())
n = len(filtered_snp_reader.sid)
# case checking
if(group_size > n):
print("trying to group more than the number of existing snps:\nprogram ended!")
exit(1)
if(group_size == 0):
print("grouping size is 0:\nprogram ended!")
exit(2)
groupNum = (n//group_size)
if (n % group_size !=0):
groupNum += 1
#print("group_num: " + str(groupNum))
if(groupNum < 2):
print("group number should be at least two, please decrease the size of snps in each group")
exit(3)
th = groupNum - 1
rest = process_id + 1
base = 0
hetero_num = groupNum*(groupNum - 1)//2
maxjobnum = hetero_num
homo_num = (groupNum //2) if (groupNum % 2 == 0) else (groupNum//2 + 1)
maxjobnum += homo_num
if(process_id >= maxjobnum):
print("job number exceeds the total number of jobs that epstasis could do")
exit(1)
list_1_idx_start = 0
list_1_idx_end = 0
list_2_idx_start = 0
list_2_idx_end = 0
single_homo = False;
#print("hetero_num: %s, homo_num: %s, maxjobnum: %s" %(hetero_num, homo_num,maxjobnum))
if(process_id < hetero_num):
while(rest > th):
rest -= th
th -= 1
base += 1
list_1_idx_start = group_size*base
list_1_idx_end = list_1_idx_start + group_size
list_2_idx_start = group_size*(base + rest)
if((base + rest) == (groupNum -1)):
list_2_idx_end = n - 1;
else:
list_2_idx_end = list_2_idx_start + group_size
#print('(' + str(base) + ',' + str(base + rest) + ')')
# homogenous computing: same group
else:
offset = process_id - hetero_num
offset *= 2
list_1_idx_start = group_size * offset
if(offset == groupNum - 1):
# last h**o with only one group
#list_1_idx_start =
list_1_idx_end = n;
single_homo = True
else:
list_1_idx_end = list_1_idx_start + group_size
list_2_idx_start = list_1_idx_end
list_2_idx_end = min(list_2_idx_start + group_size, n)
#print('(' + str(offset) + ',' + str(offset) + ')' + '(' + str(offset + 1) + ',' +\
#str(offset + 1) + ')')
# epistasis on all snps
df = None
df2 = None
if covFile:
if (process_id < hetero_num):
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, covar=covFile, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end])
else:
if(single_homo):
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, covar=covFile, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end])
else:
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, covar=covFile, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end])
df2 = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, covar=covFile, sid_list_0=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end], sid_list_1=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end])
else:
if (process_id < hetero_num):
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end])
else:
if(single_homo):
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end])
else:
df = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, sid_list_0=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end], sid_list_1=filtered_snp_reader.sid[list_1_idx_start:list_1_idx_end])
df2 = epistasis(filtered_snp_reader, pheno, G0=full_snp_reader, sid_list_0=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end], sid_list_1=filtered_snp_reader.sid[list_2_idx_start:list_2_idx_end])
def format_results(df, final_columns, threshold):
final = df.loc[:, final_columns]
final = final[final['PValue'] <= threshold]
return final
v.update(locals())
# output to csv
final = format_results(df, final_columns, p_value_threshold)
final.to_csv('%(output_dir)s/%(dataset)s_%(process_id)s.gwas' % v, sep='\t', index=False)
if(df2 is not None):
final = format_results(df2, final_columns, p_value_threshold)
final.to_csv('%(output_dir)s/%(dataset)s_%(process_id)s.gwas' % v, mode = 'a', sep='\t', index=False)
