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)