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authorLei Yan2014-02-10 15:21:44 -0600
committerLei Yan2014-02-10 15:21:44 -0600
commit37e4152e6bbf446c165faefa0220cc722c5e3c54 (patch)
tree08408aed36364f48ae843d1b64036f7f0a99dbc7 /wqflask/maintenance/dataset/specials2.py
parenta260db93da548ce7511521c5f63c03c3d279bcb1 (diff)
downloadgenenetwork2-37e4152e6bbf446c165faefa0220cc722c5e3c54.tar.gz
On branch master
Diffstat (limited to 'wqflask/maintenance/dataset/specials2.py')
-rw-r--r--wqflask/maintenance/dataset/specials2.py36
1 files changed, 33 insertions, 3 deletions
diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
index 2acfd2ef..2438af43 100644
--- a/wqflask/maintenance/dataset/specials2.py
+++ b/wqflask/maintenance/dataset/specials2.py
@@ -54,9 +54,9 @@ def bxd_correlations():
probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
for probesetfreeze in probesetfreezes:
- correlations(genos, probesetfreeze)
+ correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze)
-def correlations(genos, probesetfreeze):
+def correlations(outputdir, genos, probesetfreeze):
print probesetfreeze
probesetfreezeid = probesetfreeze[0]
probesetfreezename = probesetfreeze[1]
@@ -106,4 +106,34 @@ def correlations(genos, probesetfreeze):
outputfile.write("\n")
outputfile.flush()
#
- outputfile.close() \ No newline at end of file
+ outputfile.close()
+
+"""
+For: Ash
+Date: 2014-02-10
+Function:
+ For BXD group, calculate correlations with genotypes and probesets.
+ given probesetfreezes
+"""
+def bxd_correlations_givenprobesetfreezes(probesetfreezesfile):
+ #
+ inbredsetid = 1
+ genofile = "/home/leiyan/gn/web/genotypes/BXD.geno"
+ outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
+ #
+ t = genotypes.load_genos(genofile)
+ genostrains = t[0]
+ genos = t[1]
+ print "From geno file, get %d strains" % (len(genostrains))
+ print "From geno file, get %d genos" % (len(genos))
+ #
+ file = open(probesetfreezesfile, 'r')
+ for line in file:
+ line = line.strip()
+ cells = line.split()
+ probesetfreezeid = cells[0]
+ probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid)
+ correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze)
+ file.close()
+
+bxd_correlations_givenprobesetfreezes('/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output/probesetfreezes_filter.txt')