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| author | Lei Yan | 2014-02-05 15:42:19 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-05 15:42:19 -0600 |
| commit | 2bc4ef27ad896e3acb7049035fcf30f00f9e84e0 (patch) | |
| tree | 614ad36ebdd2d3691801615e917830c4c3deea59 | |
| parent | 2956bded432ebb92e7adf8c9821bba5885d19908 (diff) | |
| download | genenetwork2-2bc4ef27ad896e3acb7049035fcf30f00f9e84e0.tar.gz | |
On branch master
| -rw-r--r-- | wqflask/maintenance/dataset/specials.py | 13 |
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'] |