def probesetfreeze_item(strains, dir, probesetfreeze):
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
file = open("%s/ProbeSetFreezeId_%d_FullName_%s.txt" % (dir, probesetfreezeid, probesetfreezename), "w+")
file.write('"ID",')
file.write(','.join(['"%s"' % strain[1] for strain in strains]))
file.write("\n")
file.flush()
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
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)
if len(probesetdata) == 0:
continue
probesetdata = zip(*probesetdata)
probesetdata = utilities.to_dic(probesetdata[1], probesetdata[2])
#
file.write('"%s"' % probesetname)
#
for strain in strains:
strainname = strain[1]
if strainname in probesetdata:
value = probesetdata[strainname]
else:
value = ''
file.write(',"%s"' % value)
file.write('\n')
file.flush()
#
file.close()
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 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 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 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 traverse(outputfile):
#
file = open(outputfile, 'w')
inbredsetid = 1
strains = datastructure.get_strains(inbredsetid)
print("strains: %s" % len(strains))
sum = [0] * len(strains)
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
print("probesetfreezes: %s" % len(probesetfreezes))
#
cursor, con = utilities.get_cursor()
#
file.write("DatasetID\t")
file.write("DatasetName\t")
file.write("RecordNumber\t")
for strain in strains:
file.write("%s\t" % strain[1])
file.write("\n")
file.flush()
# phenotypes
publishxrefs = phenotypes.get_publishxrefs(inbredsetid)
file.write("-\t")
file.write("%s\t" % "Phenotypes")
file.write("%d\t" % len(publishxrefs))
#
for i,strain in enumerate(strains):
sql = """
SELECT COUNT(PublishData.Id)
FROM PublishXRef,PublishData
WHERE PublishXRef.InbredSetId=%s
AND PublishXRef.DataId=PublishData.Id
AND PublishData.StrainId=%s
AND PublishData.value IS NOT NULL
"""
cursor.execute(sql, (inbredsetid, strain[0]))
n = cursor.fetchone()[0]
file.write("%d\t" % n)
file.flush()
sum[i] += n
#
file.write("\n")
file.flush()
#
for probesetfreeze in probesetfreezes:
#
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
#
file.write("%d\t" % probesetfreezeid)
file.write("%s\t" % probesetfreezefullname)
file.write("%d\t" % len(probesetxrefs))
#
for i,strain in enumerate(strains):
sql = """
SELECT COUNT(ProbeSetData.`Id`)
FROM ProbeSetXRef,ProbeSetData
WHERE ProbeSetXRef.`ProbeSetFreezeId`=%s
AND ProbeSetXRef.`DataId`=ProbeSetData.`Id`
AND ProbeSetData.`StrainId`=%s
AND ProbeSetData.`value` IS NOT NULL
"""
cursor.execute(sql, (probesetfreezeid, strain[0]))
n = cursor.fetchone()[0]
file.write("%d\t" % n)
file.flush()
sum[i] += n
#
file.write("\n")
file.flush()
# sum
file.write("-\t")
file.write("%s\t" % "Sum")
file.write("-\t")
#
for e in sum:
file.write("%d\t" % e)
file.flush()
#
file.write("\n")
file.flush()
#
file.close()
con.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()
