From 94b5018690f73cfad133d2d4c81ca0e8d4a7a7d4 Mon Sep 17 00:00:00 2001
From: Lei Yan
Date: Wed, 5 Feb 2014 13:43:34 -0600
Subject: On branch master

---
 wqflask/maintenance/dataset/probesets.py | 38 ----------------------
 wqflask/maintenance/dataset/specials.py  | 56 ++++++++++++++++++++++++++++----
 2 files changed, 50 insertions(+), 44 deletions(-)

(limited to 'wqflask/maintenance/dataset')

diff --git a/wqflask/maintenance/dataset/probesets.py b/wqflask/maintenance/dataset/probesets.py
index d87240a2..97bb5bdf 100644
--- a/wqflask/maintenance/dataset/probesets.py
+++ b/wqflask/maintenance/dataset/probesets.py
@@ -1,5 +1,3 @@
-import sys
-
 import utilities
 import datastructure
 import genotypes
@@ -90,39 +88,3 @@ def get_normalized_probeset(locus, inbredsetid):
         #
         normalized_probesets.append(normalized_probeset)
     return normalized_probesets
-
-locus="rs3663871"
-inbredsetid=1
-
-results = get_normalized_probeset(locus=locus, inbredsetid=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()
-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()
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
@@ -2,6 +2,52 @@ import datastructure
 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
@@ -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")
-- 
cgit v1.2.3