On branch master

3 files changed, 162 insertions, 129 deletions

diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
deleted file mode 100644
index 4ff85333..00000000
--- a/wqflask/maintenance/dataset/specials.py
+++ /dev/null
@@ -1,129 +0,0 @@
-import utilities
-import datastructure
-import genotypes
-import probesets
-import calculate
-
-"""
-For:    Rob, GeneNetwork
-Date:   2014-02-04
-Function:
-    For BXD group, fetch probesets with given locus (mapping info).
-
-locus="rs3663871"
-"""
-def bxd_probesets_locus(locus):
-    #
-    inbredsetid=1
-    #
-    file = open('probesets_%s.txt' % (locus), 'w+')
-    file.write("GN Dataset ID\t")
-    file.write("Dataset Full Name\t")
-    file.write("ProbeSet Name\t")
-    file.write("Symbol\t")
-    file.write("ProbeSet Description\t")
-    file.write("Probe Target Description\t")
-    file.write("ProbeSet Chr\t")
-    file.write("ProbeSet Mb\t")
-    file.write("Mean\t")
-    file.write("LRS\t")
-    file.write("Geno Chr\t")
-    file.write("Geno Mb\t")
-    file.write("\n")
-    file.flush()
-    #
-    results = get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
-    for row in results:
-        file.write("%s\t" % (row[0]))
-        file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
-        file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
-        file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
-        file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
-        file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
-        file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
-        file.write("%s\t" % (row[8]))
-        file.write("%s\t" % (row[9]))
-        file.write("%s\t" % (row[10]))
-        file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
-        file.write("%s\t" % (row[12]))
-        file.write('\n')
-        file.flush()
-    file.close()
-
-"""
-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]
-    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:
-        #
-        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()
-        
-bxd_correlations()
diff --git a/wqflask/maintenance/dataset/specials1.py b/wqflask/maintenance/dataset/specials1.py
new file mode 100644
index 00000000..9159fd7f
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials1.py
@@ -0,0 +1,53 @@
+import utilities
+import datastructure
+import genotypes
+import probesets
+import calculate
+
+"""
+For:    Rob, GeneNetwork
+Date:   2014-02-04
+Function:
+    For BXD group, fetch probesets with given locus (mapping info).
+
+locus="rs3663871"
+"""
+def bxd_probesets_locus(locus, inbredsetid):
+    #
+    file = open('probesets_%s.txt' % (locus), 'w+')
+    file.write("GN Dataset ID\t")
+    file.write("Dataset Full Name\t")
+    file.write("ProbeSet Name\t")
+    file.write("Symbol\t")
+    file.write("ProbeSet Description\t")
+    file.write("Probe Target Description\t")
+    file.write("ProbeSet Chr\t")
+    file.write("ProbeSet Mb\t")
+    file.write("Mean\t")
+    file.write("LRS\t")
+    file.write("Geno Chr\t")
+    file.write("Geno Mb\t")
+    file.write("\n")
+    file.flush()
+    #
+    results = probesets.get_normalized_probeset(locus=locus, inbredsetid=inbredsetid)
+    for row in results:
+        file.write("%s\t" % (row[0]))
+        file.write("%s\t" % (utilities.clearspaces(row[2], default='')))
+        file.write("%s\t" % (utilities.clearspaces(row[3], default='')))
+        file.write("%s\t" % (utilities.clearspaces(row[4], default='')))
+        file.write("%s\t" % (utilities.clearspaces(row[5], default='')))
+        file.write("%s\t" % (utilities.clearspaces(row[6], default='')))
+        file.write("%s\t" % (utilities.clearspaces(row[7], default='')))
+        file.write("%s\t" % (row[8]))
+        file.write("%s\t" % (row[9]))
+        file.write("%s\t" % (row[10]))
+        file.write("%s\t" % (utilities.clearspaces(row[11], default='')))
+        file.write("%s\t" % (row[12]))
+        file.write('\n')
+        file.flush()
+    file.close()
+
+locus='rs3663871'
+inbredsetid=1
+bxd_probesets_locus(locus=locus, inbredsetid=inbredsetid)
diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
new file mode 100644
index 00000000..2acfd2ef
--- /dev/null
+++ b/wqflask/maintenance/dataset/specials2.py
@@ -0,0 +1,109 @@
+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