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authorLei Yan2014-02-05 15:42:19 -0600
committerLei Yan2014-02-05 15:42:19 -0600
commit2bc4ef27ad896e3acb7049035fcf30f00f9e84e0 (patch)
tree614ad36ebdd2d3691801615e917830c4c3deea59
parent2956bded432ebb92e7adf8c9821bba5885d19908 (diff)
downloadgenenetwork2-2bc4ef27ad896e3acb7049035fcf30f00f9e84e0.tar.gz
On branch master
-rw-r--r--wqflask/maintenance/dataset/specials.py13
1 files changed, 10 insertions, 3 deletions
diff --git a/wqflask/maintenance/dataset/specials.py b/wqflask/maintenance/dataset/specials.py
index 62311a92..ba9598fe 100644
--- a/wqflask/maintenance/dataset/specials.py
+++ b/wqflask/maintenance/dataset/specials.py
@@ -1,3 +1,4 @@
+import utilities
import datastructure
import genotypes
import probesets
@@ -6,7 +7,7 @@ import probesets
For: Rob, GeneNetwork
Date: 2014-02-04
Function:
- For BXD group, fetch probesets with given locus.
+ For BXD group, fetch probesets with given locus (mapping info).
locus="rs3663871"
"""
@@ -65,10 +66,11 @@ def bxd_correlations():
t = genotypes.load_genos(genofile)
genostrains = t[0]
genos = t[1]
- print "Get %d genos" % (len(genos))
+ print "From geno file, get %d strains" % (len(genostrains))
+ print "From geno file, get %d genos" % (len(genos))
#
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
- print "Get %d probesetfreezes" % (len(probesetfreezes))
+ print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
#
for probesetfreeze in probesetfreezes:
#
@@ -99,6 +101,11 @@ def bxd_correlations():
probeset = probesets.get_probeset(probesetid)
probesetname = probeset[1]
probesetdata = probesets.get_probesetdata(probesetdataid)
+ print probesetdata
+ probesetdata = zip(*probesetdata)
+ probesetdata = utilities.to_dic([strain.lower() for strain in probesetdata[1]], probesetdata[2])
+ print probesetdata
+ return
#
for geno in genos:
genoname = geno['locus']