def probesetfreeze_list(inbredsetid, dir): strains = datastructure.get_strains(inbredsetid) print(strains) probesetfreezes = datastructure.get_probesetfreezes(inbredsetid) print "From DB, get %d probesetfreezes" % (len(probesetfreezes)) for probesetfreeze in probesetfreezes: print probesetfreeze probesetfreeze_item(strains, dir, probesetfreeze)
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 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()
def traverse(outputfile): # file = open(outputfile, 'w') inbredsetid = 1 strains = datastructure.get_strains(inbredsetid) print("strains: %s" % len(strains)) sum = [0] * len(strains) probesetfreezes = datastructure.get_probesetfreezes(inbredsetid) print("probesetfreezes: %s" % len(probesetfreezes)) # cursor, con = utilities.get_cursor() # file.write("DatasetID\t") file.write("DatasetName\t") file.write("RecordNumber\t") for strain in strains: file.write("%s\t" % strain[1]) file.write("\n") file.flush() # phenotypes publishxrefs = phenotypes.get_publishxrefs(inbredsetid) file.write("-\t") file.write("%s\t" % "Phenotypes") file.write("%d\t" % len(publishxrefs)) # for i,strain in enumerate(strains): sql = """ SELECT COUNT(PublishData.Id) FROM PublishXRef,PublishData WHERE PublishXRef.InbredSetId=%s AND PublishXRef.DataId=PublishData.Id AND PublishData.StrainId=%s AND PublishData.value IS NOT NULL """ cursor.execute(sql, (inbredsetid, strain[0])) n = cursor.fetchone()[0] file.write("%d\t" % n) file.flush() sum[i] += n # file.write("\n") file.flush() # for probesetfreeze in probesetfreezes: # probesetfreezeid = probesetfreeze[0] probesetfreezename = probesetfreeze[1] probesetfreezefullname = probesetfreeze[2] probesetxrefs = probesets.get_probesetxref(probesetfreezeid) # file.write("%d\t" % probesetfreezeid) file.write("%s\t" % probesetfreezefullname) file.write("%d\t" % len(probesetxrefs)) # for i,strain in enumerate(strains): sql = """ SELECT COUNT(ProbeSetData.`Id`) FROM ProbeSetXRef,ProbeSetData WHERE ProbeSetXRef.`ProbeSetFreezeId`=%s AND ProbeSetXRef.`DataId`=ProbeSetData.`Id` AND ProbeSetData.`StrainId`=%s AND ProbeSetData.`value` IS NOT NULL """ cursor.execute(sql, (probesetfreezeid, strain[0])) n = cursor.fetchone()[0] file.write("%d\t" % n) file.flush() sum[i] += n # file.write("\n") file.flush() # sum file.write("-\t") file.write("%s\t" % "Sum") file.write("-\t") # for e in sum: file.write("%d\t" % e) file.flush() # file.write("\n") file.flush() # file.close() con.close()