Merge /home/lei/gene

1 files changed, 117 insertions, 0 deletions

diff --git a/wqflask/maintenance/dataset/specials3.py b/wqflask/maintenance/dataset/specials3.py
new file mode 100644
index 00000000..237df27e
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials3.py
@@ -0,0 +1,117 @@
+import utilities
+import datastructure
+import genotypes
+import probesets
+import calculate
+
+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:   2014-02-12
+Function:
+    Generate probeset data files.
+    given probesetfreeze list.
+"""
+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()
+
+probesetfreezesfile = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output2/probesetfreezes_filter.txt"
+outputdir           = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output2"
+generate_probesets(probesetfreezesfile, outputdir)