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Diffstat (limited to 'wqflask/maintenance/dataset/specials2.py')
| -rw-r--r-- | wqflask/maintenance/dataset/specials2.py | 109 |
1 files changed, 109 insertions, 0 deletions
diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py new file mode 100644 index 00000000..2acfd2ef --- /dev/null +++ b/wqflask/maintenance/dataset/specials2.py @@ -0,0 +1,109 @@ +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(genos, probesetfreeze) + +def correlations(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()
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