def get_normalized_probeset(locus, inbredsetid):
normalized_probesets = []
probesetxrefs = get_probesetxref_inbredsetid(locus, inbredsetid)
for probesetxref in probesetxrefs:
normalized_probeset = []
#
probesetfreezeid = probesetxref[4]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
normalized_probeset.append(probesetfreeze[0])
normalized_probeset.append(probesetfreeze[1])
normalized_probeset.append(probesetfreeze[2])
#
probesetid = probesetxref[0]
probeset = get_probeset(probesetid)
normalized_probeset.append(probeset[1])
normalized_probeset.append(probeset[2])
normalized_probeset.append(probeset[3])
normalized_probeset.append(probeset[4])
normalized_probeset.append(probeset[5])
normalized_probeset.append(probeset[6])
#
normalized_probeset.append(probesetxref[1])
normalized_probeset.append(probesetxref[2])
#
locus = probesetxref[3]
geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus)
normalized_probeset.append(geno[2])
normalized_probeset.append(geno[3])
#
normalized_probesets.append(normalized_probeset)
return normalized_probesets
def bxd_givenprobesetfreezes(probesetfreezesfile):
file = open(probesetfreezesfile, 'r')
for line in file:
line = line.strip()
cells = line.split()
probesetfreezeid = cells[0]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print "%s\t%s\t%s\t%d" % (probesetfreezeid, probesetfreezename, probesetfreezefullname, len(probesetxrefs))
file.close()
def generate_probesets(probesetfreezesfile, outputdir):
file = open(probesetfreezesfile, 'r')
for line in file:
line = line.strip()
cells = line.split()
probesetfreezeid = cells[0]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
inbredset = datastructure.get_inbredset(probesetfreezeid)
inbredsetid = inbredset[0]
strains = datastructure.get_strains(inbredsetid)
#
outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
outputfile.write("%s\t" % "ProbeSet Id")
outputfile.write("%s\t" % "ProbeSet Name")
outputfile.write('\t'.join([strain[1].upper() for strain in strains]))
outputfile.write("\n")
outputfile.flush()
#
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print probesetfreeze
print 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])
#
outputfile.write("%s\t" % probesetid)
outputfile.write("%s\t" % probesetname)
#
for strain in strains:
strainname = strain[1]
strainname = strainname.lower()
if strainname in probesetdata:
value = probesetdata[strainname]
else:
value = 'x'
outputfile.write("%s\t" % value)
outputfile.write("\n")
outputfile.flush()
#
outputfile.close()
file.close()
def bxd_correlations_givenprobesetfreezes(probesetfreezesfile, outputdir):
#
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))
#
file = open(probesetfreezesfile, 'r')
for line in file:
line = line.strip()
cells = line.split()
probesetfreezeid = cells[0]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze)
file.close()
def generate_probesets(probesetfreezesfile, outputdir):
file = open(probesetfreezesfile, 'r')
for line in file:
line = line.strip()
cells = line.split()
probesetfreezeid = cells[0]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
#
outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
outputfile.write("%s\t" % "ProbeSetId")
outputfile.write("%s\t" % "ProbeSetName")
outputfile.write("%s\t" % "Symbol")
outputfile.write("%s\t" % "StrainNumbers")
outputfile.write("\n")
outputfile.flush()
#
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print probesetfreeze
print len(probesetxrefs)
for probesetxref in probesetxrefs:
probesetid = probesetxref[0]
probesetdataid = probesetxref[1]
probeset = probesets.get_probeset(probesetid)
probesetname = probeset[1]
probesetsymbol = probeset[2]
probesetdescription = probeset[3]
probesetchr = probeset[5]
probesetmb = probeset[6]
probesetdata = probesets.get_probesetdata(probesetdataid)
#
outputfile.write("%s\t" % probesetid)
outputfile.write("%s\t" % probesetname)
outputfile.write("%s\t" % probesetsymbol)
outputfile.write("%d" % len(probesetdata))
outputfile.write("\n")
outputfile.flush()
#
outputfile.close()
file.close()
def generate_probesets_2(probesetfreezesfile, outputdir):
file = open(probesetfreezesfile, 'r')
for line in file:
line = line.strip()
cells = line.split()
probesetfreezeid = cells[0]
probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
inbredset = datastructure.get_inbredset(probesetfreezeid)
inbredsetid = inbredset[0]
#
outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
outputfile.write("%s\t" % "ProbeSetId")
outputfile.write("%s\t" % "Symbol")
outputfile.write("%s\t" % "Description")
outputfile.write("%s\t" % "Chr")
outputfile.write("%s\t" % "MB")
outputfile.write("%s\t" % "Marker_Chr")
outputfile.write("%s\t" % "Marker_MB")
outputfile.write("%s\t" % "Mean_Expression")
outputfile.write("%s\t" % "SE")
outputfile.write("%s\t" % "LRS")
outputfile.write("%s\t" % "pValue")
outputfile.write("\n")
outputfile.flush()
#
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
print("%s:\n\t%d probesetxrefs" % (probesetfreeze, len(probesetxrefs)))
for probesetxref in probesetxrefs:
#
probesetid = probesetxref[0]
locus = probesetxref[2]
lrs = probesetxref[3]
pvalue = probesetxref[4]
mean = probesetxref[5]
se = probesetxref[6]
#
probeset = probesets.get_probeset(probesetid)
probesetname = probeset[1]
probesetsymbol = probeset[2]
probesetdescription = probeset[3]
probesetchr = probeset[5]
probesetmb = probeset[6]
#
if locus is None or not locus:
genochr = ""
genomb = ""
else:
geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus)
genochr = geno[2]
genomb = geno[3]
#
outputfile.write("%s\t" % probesetname)
outputfile.write("%s\t" % probesetsymbol)
outputfile.write("%s\t" % probesetdescription)
outputfile.write("%s\t" % probesetchr)
outputfile.write("%s\t" % probesetmb)
outputfile.write("%s\t" % genochr)
outputfile.write("%s\t" % genomb)
outputfile.write("%s\t" % mean)
outputfile.write("%s\t" % se)
outputfile.write("%s\t" % lrs)
outputfile.write("%s\t" % pvalue)
outputfile.write("\n")
outputfile.flush()
#
outputfile.close()
file.close()