def run_vcf_to_calc(f_in, f_out):
args = [
f_in, '--calc-statistic', 'windowed-weir-fst', '--out-prefix',
'merged_chr1_10000', '--model-file', 'input.model', '--model', '2Pop',
'--overwrite'
]
vcf_calc.run(args)
def run_vcf_to_calc8(f_in, f_out):
args = [
f_in, '--calc-statistic', 'TajimaD', '--out-prefix',
'merged_chr1_10000.2', '--model-file', 'input.model', '--model',
'2Pop', '--overwrite'
]
#print (f_in)
#print (args)
vcf_calc.run(args)
def test_freq(self):
# Run the function with the following arguments
vcf_calc.run([
'merged_chr1_1000.vcf.gz', '--calc-statistic', 'freq', '--out',
'out'
])
# Confirm that the output is what is expected
#self.assertTrue(file_comp('out.frq', 'example/merged_chr1_10000.frq'))
# Confirm that the output is what is expected
self.assertTrue(os.path.isfile('out.frq'))
self.assertTrue(os.path.isfile('out.frq.log'))
def run_vcf_to_calc1(f_in,f_out):
for i in range(len(list2)):
print (len(list2))
args = ['merged_chr1_10000.recode.bcf']+calc_final_list[123]
#args = newpath[1]+"/merged_chr1_10000.recode.bcf"+calc_final_list[123]
print (f_in)
print (args)
vcf_calc.run(args)
print ('hello')
print (newpath[i])
shutil.move('merged_chr1_10000'+name2, newpath[i])
shutil.move('merged_chr1_10000'+name2+'.log', newpath[i])
shutil.move('/home/staff/asukeshkall/Downloads/Test-3/Run/test2/merged_chr1_10000.windowed.weir.fst','/home/staff/asukeshkall/Downloads/Test-3/')
def run_vcf_to_calc(f_in, f_out):
a1 = [f_in]
b1 = []
c1 = []
for i in range(len(unmatched1)):
b1 = unmatched1[i]
b1.insert(0, a1[0])
c1.append(b1)
for t in c1:
print t
vcf_calc.run(c1[11])
self.assertTrue(
os.path.isfile('merged_chr1_1000.windowed.weir.fst'))
self.assertTrue(
os.path.isfile('merged_chr1_1000.windowed.weir.fst.log'))
def winWeirFuncCall(index):
vcf_calc.run(winWeirList[index])
winWeirFunc('out',index,winWeirPath)
vcf_calc.run(outWinWeirList[index])
winWeirFunc('out',index,outWinWeirPath)
vcf_calc.run(resWinWeirList[index])
winWeirFunc('res',index,resWinWeirPath)
def hetFuncCall(index):
vcf_calc.run(hetList[index])
hetFunc('out',index,hetPath)
vcf_calc.run(outHetList[index])
hetFunc('out',index,outHetPath)
vcf_calc.run(resHetList[index])
hetFunc('res',index,resHetPath)
def freqFuncCall(index):
vcf_calc.run(freqList[index])
freqFunc('out',index,freqPath)
vcf_calc.run(outFreqList[index])
freqFunc('out',index,outFreqPath)
vcf_calc.run(resFreqList[index])
freqFunc('res',index,resFreqPath)
def piFuncCall(index):
vcf_calc.run(piList[index])
piFunc('out',index,piPath)
vcf_calc.run(outPiList[index])
piFunc('out',index,outPiPath)
vcf_calc.run(resPiList[index])
piFunc('res',index,resPiPath)
def tajimaFuncCall(index):
vcf_calc.run(tajimaList[index])
tajimaFunc('out',index,tajimaPath)
vcf_calc.run(outTajimaList[index])
tajimaFunc('out',index,outTajimaPath)
vcf_calc.run(resTajimaList[index])
tajimaFunc('res',index,resTajimaPath)
def run_vcf_to_calc(f_in,f_out):
args = [f_in]+calc_final_list[123]
#args = newpath[1]+"/merged_chr1_10000.recode.bcf"+calc_final_list[123]
print f_in
print args
vcf_calc.run(args)
def defaultFuncCall(index,):
vcf_calc.run(defList[index])
defaultFunc('out',index,defaultPath)
def run_vcf_to_calc(f_in,f_out):
args = [f_in,
'--calc-statistic', 'freq',
'--out', 'out']
vcf_calc.run(args)
