On branch master

1 files changed, 50 insertions, 6 deletions

diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
index 52a2389f..90ab1c5f 100644
--- a/wqflask/maintenance/dataset/specials.py
+++ b/wqflask/maintenance/dataset/specials.py
@@ -3,6 +3,52 @@ import genotypes
 import probesets
 
 """
+For:    Rob, GeneNetwork
+Date:   2014-02-04
+Function:
+    For BXD group, fetch probesets with given locus.
+
+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:
@@ -50,16 +96,14 @@ def bxd_correlations():
             probesetid = probesetxref[0]
             probesetdataid = probesetxref[1]
             probeset = probesets.get_probeset(probesetid)
-            ProbeSetId = probeset[0]
-            ProbeSetName = probeset[1]
-            # Geno Name       Overlap Number  Pearson r       Pearson p       Spearman r      Spearman p
+            probesetname = probeset[1]
             probesetdata = probesets.get_probesetdata(probesetdataid)
             #
             for geno in genos:
                 genoname = geno['locus']
-                outputfile.write("%s\t" % probeSetid)
-                outputfile.write("%s\t" % ProbeSetName)
-                outputfile.write("%s\t" % GenoName)
+                outputfile.write("%s\t" % probesetid)
+                outputfile.write("%s\t" % probesetname)
+                outputfile.write("%s\t" % genoname)
                 outputfile.write("%s\t" % "Overlap Number")
                 outputfile.write("%s\t" % "Pearson r")
                 outputfile.write("%s\t" % "Pearson p")