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Diffstat (limited to 'wqflask/maintenance/dataset/specials2.py')
| -rw-r--r-- | wqflask/maintenance/dataset/specials2.py | 139 |
1 files changed, 0 insertions, 139 deletions
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') |