On branch master

1 files changed, 56 insertions, 0 deletions

diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
index e69de29b..9caba879 100644
--- a/wqflask/maintenance/dataset/specials.py
+++ b/wqflask/maintenance/dataset/specials.py
@@ -0,0 +1,56 @@
+import datastructure
+import genotypes
+import probesets
+
+"""
+For:    Ash
+Date:   2014-02-05
+Function:
+    For BXD group, calculate correlations with genotypes and probesets.
+Running History:
+    2014-02-05  /home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output
+"""
+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]
+    #
+    probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
+    print "Get %d probesetfreezes" % (len(probesetfreezes))
+    #
+    for probesetfreeze in probesetfreezes:
+        #
+        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)
+            probesetdata = probesets.get_probesetdata(probesetdataid)
+        #
+        outputfile.close()
+        
+bxd_correlations()