Merge /home/lei/gene

1 files changed, 53 insertions, 0 deletions

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)