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authorLei Yan2014-02-10 14:59:27 -0600
committerLei Yan2014-02-10 14:59:27 -0600
commita260db93da548ce7511521c5f63c03c3d279bcb1 (patch)
tree50965c7995bdadc6b104fa05f074d7494e1d872e /wqflask/maintenance/dataset/specials2.py
parent4093f244cad0bd5ba21412acd9dfd1589db2d761 (diff)
downloadgenenetwork2-a260db93da548ce7511521c5f63c03c3d279bcb1.tar.gz
On branch master
Diffstat (limited to 'wqflask/maintenance/dataset/specials2.py')
-rw-r--r--wqflask/maintenance/dataset/specials2.py109
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diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
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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(genos, probesetfreeze)
+
+def correlations(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() \ No newline at end of file