aboutsummaryrefslogtreecommitdiff
path: root/wqflask/maintenance/dataset
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/maintenance/dataset')
-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']