Merge /home/lei/gene

1 files changed, 139 insertions, 0 deletions

diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
new file mode 100644
index 00000000..2438af43
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials2.py
@@ -0,0 +1,139 @@
+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')