def correlations(outputdir, genos, probesetfreeze):
print probesetfreeze
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
#
outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
outputfile.write("%s\t" % "ProbeSet Id")
outputfile.write("%s\t" % "ProbeSet Name")
outputfile.write("%s\t" % "Geno Name")
outputfile.write("%s\t" % "Overlap Number")
outputfile.write("%s\t" % "Pearson r")
outputfile.write("%s\t" % "Pearson p")
outputfile.write("%s\t" % "Spearman r")
outputfile.write("%s\t" % "Spearman p")
outputfile.write("\n")
outputfile.flush()
#
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print "Get %d probesetxrefs" % (len(probesetxrefs))
#
for probesetxref in probesetxrefs:
#
probesetid = probesetxref[0]
probesetdataid = probesetxref[1]
probeset = probesets.get_probeset(probesetid)
probesetname = probeset[1]
probesetdata = probesets.get_probesetdata(probesetdataid)
probesetdata = zip(*probesetdata)
probesetdata = utilities.to_dic([strain.lower() for strain in probesetdata[1]], probesetdata[2])
#
for geno in genos:
genoname = geno['locus']
outputfile.write("%s\t" % probesetid)
outputfile.write("%s\t" % probesetname)
outputfile.write("%s\t" % genoname)
#
dic1 = geno['dicvalues']
dic2 = probesetdata
keys, values1, values2 = utilities.overlap(dic1, dic2)
rs = calculate.correlation(values1, values2)
#
outputfile.write("%s\t" % len(keys))
outputfile.write("%s\t" % rs[0][0])
outputfile.write("%s\t" % rs[0][1])
outputfile.write("%s\t" % rs[1][0])
outputfile.write("%s\t" % rs[1][1])
outputfile.write("\n")
outputfile.flush()
#
outputfile.close()
def bxd_geno_pheno_correlations(file):
#
file = open(file, 'w')
inbredsetid = 1
genofile = "/home/leiyan/gn/web/genotypes/BXD.geno"
#
t = genotypes.load_genos(genofile)
genostrains = t[0]
genos = t[1]
print("From geno file, get %d strains" % (len(genostrains)))
print("From geno file, get %d genos" % (len(genos)))
#
publishxrefs = phenotypes.get_publishxrefs(inbredsetid)
print("get %d publishxrefs" % (len(publishxrefs)))
#
file.write("%s\t" % "PhenotypeID")
file.write("%s\t" % "PhenotypeName")
file.write("%s\t" % "MarkerName")
file.write("%s\t" % "MarkerChromosome")
file.write("%s\t" % "MarkerCentimorgan")
file.write("%s\t" % "MarkerMb")
file.write("%s\t" % "PearsonCorrelation")
file.write("%s\t" % "PearsonPvalue")
file.write("%s\t" % "SpearmanCorrelation")
file.write("%s\t" % "SpearmanPvalue")
file.write("%s\t" % "Number_of_BXDs_used")
file.write("\n")
file.flush()
#
for publishxref in publishxrefs:
#
publishxrefid = publishxref[0]
phenotypeid = publishxref[1]
phenotype = phenotypes.get_phenotype(phenotypeid)
publicationid = publishxref[2]
publication = phenotypes.get_publication(publicationid)
publishdataid = publishxref[3]
publishdata = phenotypes.get_publishdata(publishdataid)
publishdata = zip(*publishdata)
if len(publishdata) != 3:
print("publishdata - %s: %d" % (publishxrefid, len(publishdata)))
continue
publishdata = utilities.to_dic([strain.lower() for strain in publishdata[1]], publishdata[2])
#
for geno in genos:
#
dic1 = geno['dicvalues']
dic2 = publishdata
keys, values1, values2 = utilities.overlap(dic1, dic2)
rs = calculate.correlation(values1, values2)
#
file.write("%s\t" % publishxrefid)
file.write("%s;%s;%s\t" % (phenotype[0], phenotype[1], phenotype[2]))
file.write("%s\t" % geno['locus'])
file.write("%s\t" % geno['chr'])
file.write("%s\t" % geno['cm'])
file.write("%s\t" % geno['mb'])
file.write("%s\t" % rs[0][0])
file.write("%s\t" % rs[0][1])
file.write("%s\t" % rs[1][0])
file.write("%s\t" % rs[1][1])
file.write("%s\t" % len(keys))
file.write("\n")
file.flush()
#
file.close()