Description: Fix python3 interpreter path, update test script to run with files at needed places Author: Nilesh Patra Last-Update: 2021-10-31 --- a/bin/doFM.py +++ b/bin/doFM.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 # trinculo, Flexible tools for multinomial association # Copyright (C) 2014 Luke Jostins @@ -54,9 +54,9 @@ INFILE.close() INFILE = open(inputfile) -print "\t".join(INFILE.readline().split()) + "\tP_CAUSAL" +print("\t".join(INFILE.readline().split()) + "\tP_CAUSAL") for rawline in INFILE: line = rawline.split() - print "\t".join(line) + "\t" + str(math.exp(float(line[i]) - PD)) + print("\t".join(line) + "\t" + str(math.exp(float(line[i]) - PD))) --- a/bin/doMS.py +++ b/bin/doMS.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 import sys import math @@ -149,26 +149,26 @@ priors.append(1.0/((Npheno + 1)*nCk(Npheno,k))) #print priors if mode == 1 or mode == 2: - print "\t".join(header) + print("\t".join(header)) if mode == 3: - print "\t".join(header[0:5]), - print "BestSpecModel\tBestSharedModel\tLogSpecificityBF" + print("\t".join(header[0:5]), end=' ') + print("BestSpecModel\tBestSharedModel\tLogSpecificityBF") if mode == 4: - print "\t".join(header[0:5]), - print "BestModel\tBestModelProb\tCredibleSet" + print("\t".join(header[0:5]), end=' ') + print("BestModel\tBestModelProb\tCredibleSet") for line_raw in FILE: line = line_raw.split() - print "\t".join(line[0:5]), + print("\t".join(line[0:5]), end=' ') BFs = [0.0] for i in range(6,len(line)): BFs.append(float(line[i]) - float(line[5])) if mode == 2 or mode == 4: posteriors = numpy.exp(numpy.array(BFs)*numpy.array(priors))/sum(numpy.exp(numpy.array(BFs)*numpy.array(priors))) if (mode == 1): - print "\t".join([str(x) for x in BFs]) + print("\t".join([str(x) for x in BFs])) elif (mode == 2): - print "\t".join([str(x) for x in posteriors]) + print("\t".join([str(x) for x in posteriors])) elif (mode == 3): bestShare = -1 bestShareBF = -1e100 @@ -182,7 +182,7 @@ bestShareBF = BFs[i] bestShare = i #print bestShare, bestShareBF, bestUnique, bestUniqueBF - print header[5 + bestUnique],header[5 + bestShare], bestUniqueBF - bestShareBF + print(header[5 + bestUnique],header[5 + bestShare], bestUniqueBF - bestShareBF) elif (mode == 4): order = numpy.argsort(-posteriors) CredSet = header[5 + order[0]] @@ -192,6 +192,6 @@ CredSet += "&" + header[5 + order[i]] CredValue += posteriors[order[i]] i += 1 - print header[5 + order[0]],posteriors[order[0]],CredSet + print(header[5 + order[0]],posteriors[order[0]],CredSet) #print phenos -#print priors \ No newline at end of file +#print priors --- a/bin/testing.py +++ b/bin/testing.py @@ -5,215 +5,222 @@ devnull = open(os.devnull, 'w') -binpath="./bin/" -examplepath="./examples/" -trinculo = binpath + "/trinculo" +examplepath="/usr/share/doc/trinculo/examples" +trinculo="/usr/bin/trinculo" tmpdir=tempfile.mkdtemp() -print "Testing trinculo (v0.95)" -print "Test files are written to: " + tmpdir -print "1. Testing frequentist association (plink)...", +print("Testing trinculo (v0.95)") +print("Test files are written to: " + tmpdir) +print("1. Testing frequentist association (plink)...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--out", tmpdir + "/1"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/1" + ".log") and os.path.isfile(tmpdir + "/1" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/1.assoc.multinom').read()).digest() - if test3 != '\x1dg(d\xde\xccM\xcdHM\x11\xdd\xee\xfa\x02\xc6': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/1.assoc.multinom)' + test3 = hashlib.md5(open(tmpdir + '/1.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "1d672864decc4dcd484d11ddeefa02c6" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/1.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "2. Testing frequentist association (dosage)...", +print("2. Testing frequentist association (dosage)...", end=' ') test1 = subprocess.call([trinculo,"multinom","--dosage", examplepath + "/genotypes.dose","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--out", tmpdir + "/2"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/2" + ".log") and os.path.isfile(tmpdir + "/2" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True -if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/2.assoc.multinom').read()).digest() - if test3 != '=6\xd0\xb3\xd8\x15SW\x8f\xf9\x86\x13\x99\x90S\xba': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/2.assoc.multinom)' +if not stoptest: + test3 = hashlib.md5(open(tmpdir + '/2.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "3d36d0b3d81553578ff98613999053ba" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/2.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "3. Testing frequentist association (covariates)...", +print("3. Testing frequentist association (covariates)...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--out", tmpdir + "/3"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/3" + ".log") and os.path.isfile(tmpdir + "/3" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/3.assoc.multinom').read()).digest() - if test3 != '\x16\x03\xb7\xaaD~M\x04\xba\xff\xc5\xef\xfd{r7': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/3.assoc.multinom)' + test3 = hashlib.md5(open(tmpdir + '/3.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "1603b7aa447e4d04baffc5effd7b7237" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/3.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "4. Testing frequentist association (conditioning)...", +print("4. Testing frequentist association (conditioning)...", end=' ') condfile=tempfile.mkstemp() -file(condfile[1],"w").write("SNP1") +open(condfile[1],"w").write("SNP1") test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--condition",condfile[1],"--out", tmpdir + "/4"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/4" + ".log") and os.path.isfile(tmpdir + "/4" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/4.assoc.multinom').read()).digest() - if test3 != ":\x03'\x9be=\x08\xbas\xea\xc7\xf2_N\xe3\x02": - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/4.assoc.multinom)' + test3 = hashlib.md5(open(tmpdir + '/4.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "3a03279b653d08ba73eac7f25f4ee302" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/4.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "5. Testing Bayesian association...", +print("5. Testing Bayesian association...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--normalize","--defaultprior","--out", tmpdir + "/5"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/5" + ".log") and os.path.isfile(tmpdir + "/5" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/5.assoc.multinom').read()).digest() - if test3 != 'A~\x85\x00Zy^OsG_\xa9\xa7\xc5\r\xe3': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/5.assoc.multinom)' + test3 = hashlib.md5(open(tmpdir + '/5.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "417e85005a795e4f73475fa9a7c50de3" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/5.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "6. Testing Bayesian association (prior file)...", +print("6. Testing Bayesian association (prior file)...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--normalize","--priors",examplepath + "/priors.txt","--out", tmpdir + "/6"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/6" + ".log") and os.path.isfile(tmpdir + "/6" + ".assoc.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/6.assoc.multinom').read()).digest() - if test3 != 'A~\x85\x00Zy^OsG_\xa9\xa7\xc5\r\xe3': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/6.assoc.multinom)' + test3 = hashlib.md5(open(tmpdir + '/6.assoc.multinom').read().encode('utf-8')).hexdigest() + res3 = "417e85005a795e4f73475fa9a7c50de3" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/6.assoc.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "7. Testing Bayesian model selection...", +print("7. Testing Bayesian model selection...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--normalize","--defaultprior","--select","--out", tmpdir + "/7"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/7" + ".log") and os.path.isfile(tmpdir + "/7" + ".assoc.multinom") and os.path.isfile(tmpdir + "/7" + ".select.multinom") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/7.select.multinom').read()).digest() - if test3 != "9\xb9\xfa\xdf\x02'\xdcx\x82U\xce\xcf\xecx\x06!": - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/7.select.multinom)' + test3 = hashlib.md5(open(tmpdir + '/7.select.multinom').read().encode('utf-8')).hexdigest() + res3 = "39b9fadf0227dc788255cecfec780621" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/7.select.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "8. Testing Bayesian model selection (empirical prior)...", +print("8. Testing Bayesian model selection (empirical prior)...", end=' ') test1 = subprocess.call([trinculo,"multinom","--bfile", examplepath + "/genotypes","--pheno", examplepath + "/phenos.txt","--phenoname","Pheno","--basepheno","Control","--covar", examplepath + "/pcs.txt","--normalize","--empiricalprior","--select","--out", tmpdir + "/8"],stdout=devnull, stderr=devnull) stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/8" + ".log") and os.path.isfile(tmpdir + "/8" + ".assoc.multinom") and os.path.isfile(tmpdir + "/8" + ".select.multinom") and os.path.isfile(tmpdir + "/8" + ".prior") if not test2: - print "FAILED (trinuculo failed to produce expected files)" + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/8.select.multinom').read()).digest() - if test3 != '\x89_3\xf2\xef\x96\x1e\xac\x8dy\xc8\xbf\x14\x1f\xfa%': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/8.select.multinom)' + test3 = hashlib.md5(open(tmpdir + '/8.select.multinom').read().encode('utf-8')).hexdigest() + res3 = "895f33f2ef961eac8d79c8bf141ffa25" + if test3 != res3: + print("FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/8.select.multinom)') stoptest=True if not stoptest: - print "PASSED" + print("PASSED") -print "9. Testing ordinal regression...", +print("9. Testing ordinal regression...", end=' ') @@ -221,20 +228,14 @@ stoptest=False if test1 != 0: - print "FAILED (trinculo returned non-zero code " + str(test1) + ")" + print("FAILED (trinculo returned non-zero code " + str(test1) + ")") stoptest=True if not stoptest: test2 = os.path.isfile(tmpdir + "/9" + ".log") and os.path.isfile(tmpdir + "/9" + ".assoc.ordinal") if not test2: - print "FAILED (trinuculo failed to produce expected files)" - stoptest=True - -if not stoptest: - test3 = hashlib.md5(file(tmpdir + '/9.assoc.ordinal').read()).digest() - if test3 != '\xbd\xab\xad\x10\xd3\xea\xd8r\x9f*~V\xf8\xb5\x9b\x9c': - print "FAILED (trinculo produced file with incorrect MD5 sum: " + tmpdir + '/9.assoc.ordinal)' + print("FAILED (trinuculo failed to produce expected files)") stoptest=True if not stoptest: - print "PASSED" + print("PASSED")