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import utilities
import datastructure
import genotypes
import probesets
import calculate
"""
For: Ash
Date: 2014-02-07
Function:
For BXD group, get a probesetfreeze name list.
"""
def probesetfreeze_list():
#
inbredsetid = 1
outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
#
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
file = open(outputdir + '/' + 'probesetfreezes.txt', 'w+')
#
for probesetfreeze in probesetfreezes:
#
print probesetfreeze
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
probesetfreezefullname = probesetfreeze[2]
#
file.write("%s\t" % probesetfreezeid)
file.write("%s" % probesetfreezefullname)
file.write("\n")
file.flush()
#
file.close()
"""
For: Ash
Date: 2014-02-05
Function:
For BXD group, calculate correlations with genotypes and probesets.
"""
def bxd_correlations():
#
inbredsetid = 1
genofile = "/home/leiyan/gn/web/genotypes/BXD.geno"
outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
#
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))
#
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
for probesetfreeze in probesetfreezes:
correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze)
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()
"""
For: Ash
Date: 2014-02-10
Function:
For BXD group, calculate correlations with genotypes and probesets.
given probesetfreezes
"""
def bxd_correlations_givenprobesetfreezes(probesetfreezesfile):
#
inbredsetid = 1
genofile = "/home/leiyan/gn/web/genotypes/BXD.geno"
outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
#
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()
bxd_correlations_givenprobesetfreezes('/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output/probesetfreezes_filter.txt')
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