From fca37195705ac68f21a1f725cf1fe3c59e0d1800 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 26 Jan 2016 19:08:13 +0000
Subject: Removed a bunch of files/directories/packages that are no longer used
 and some corresponding imports

---
 wqflask/maintenance/dataset/specials2.py | 139 -------------------------------
 1 file changed, 139 deletions(-)
 delete mode 100644 wqflask/maintenance/dataset/specials2.py

(limited to 'wqflask/maintenance/dataset/specials2.py')

diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py
deleted file mode 100644
index 2438af43..00000000
--- a/wqflask/maintenance/dataset/specials2.py
+++ /dev/null
@@ -1,139 +0,0 @@
-import utilities
-import datastructure
-import genotypes
-import probesets
-import calculate
-
-"""
-For:    Ash
-Date:   2014-02-07
-Function:
-    For BXD group, get a probesetfreeze name list.
-"""
-def probesetfreeze_list():
-    #
-    inbredsetid = 1
-    outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output"
-    #
-    probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
-    print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
-    file = open(outputdir + '/' + 'probesetfreezes.txt', 'w+')
-    #
-    for probesetfreeze in probesetfreezes:
-        #
-        print probesetfreeze
-        probesetfreezeid = probesetfreeze[0]
-        probesetfreezename = probesetfreeze[1]
-        probesetfreezefullname = probesetfreeze[2]
-        #
-        file.write("%s\t" % probesetfreezeid)
-        file.write("%s" % probesetfreezefullname)
-        file.write("\n")
-        file.flush()
-        #
-    file.close()
-        
-"""
-For:    Ash
-Date:   2014-02-05
-Function:
-    For BXD group, calculate correlations with genotypes and probesets.
-"""
-def bxd_correlations():
-    #
-    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))
-    #
-    probesetfreezes = datastructure.get_probesetfreezes(inbredsetid)
-    print "From DB, get %d probesetfreezes" % (len(probesetfreezes))
-    for probesetfreeze in probesetfreezes:
-        correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze)
-    
-def correlations(outputdir, genos, probesetfreeze):
-    print probesetfreeze
-    probesetfreezeid = probesetfreeze[0]
-    probesetfreezename = probesetfreeze[1]
-    probesetfreezefullname = probesetfreeze[2]
-    #
-    outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+")
-    outputfile.write("%s\t" % "ProbeSet Id")
-    outputfile.write("%s\t" % "ProbeSet Name")
-    outputfile.write("%s\t" % "Geno Name")
-    outputfile.write("%s\t" % "Overlap Number")
-    outputfile.write("%s\t" % "Pearson r")
-    outputfile.write("%s\t" % "Pearson p")
-    outputfile.write("%s\t" % "Spearman r")
-    outputfile.write("%s\t" % "Spearman p")
-    outputfile.write("\n")
-    outputfile.flush()
-    #
-    probesetxrefs = probesets.get_probesetxref(probesetfreezeid)
-    print "Get %d probesetxrefs" % (len(probesetxrefs))
-    #
-    for probesetxref in probesetxrefs:
-        #
-        probesetid = probesetxref[0]
-        probesetdataid = probesetxref[1]
-        probeset = probesets.get_probeset(probesetid)
-        probesetname = probeset[1]
-        probesetdata = probesets.get_probesetdata(probesetdataid)
-        probesetdata = zip(*probesetdata)
-        probesetdata = utilities.to_dic([strain.lower() for strain in probesetdata[1]], probesetdata[2])
-        #
-        for geno in genos:
-            genoname = geno['locus']
-            outputfile.write("%s\t" % probesetid)
-            outputfile.write("%s\t" % probesetname)
-            outputfile.write("%s\t" % genoname)
-            #
-            dic1 = geno['dicvalues']
-            dic2 = probesetdata
-            keys, values1, values2 = utilities.overlap(dic1, dic2)
-            rs = calculate.correlation(values1, values2)
-            #
-            outputfile.write("%s\t" % len(keys))
-            outputfile.write("%s\t" % rs[0][0])
-            outputfile.write("%s\t" % rs[0][1])
-            outputfile.write("%s\t" % rs[1][0])
-            outputfile.write("%s\t" % rs[1][1])
-            outputfile.write("\n")
-            outputfile.flush()
-    #
-    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')
-- 
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