def get_normalized_probeset(locus, inbredsetid): normalized_probesets = [] probesetxrefs = get_probesetxref_inbredsetid(locus, inbredsetid) for probesetxref in probesetxrefs: normalized_probeset = [] # probesetfreezeid = probesetxref[4] probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) normalized_probeset.append(probesetfreeze[0]) normalized_probeset.append(probesetfreeze[1]) normalized_probeset.append(probesetfreeze[2]) # probesetid = probesetxref[0] probeset = get_probeset(probesetid) normalized_probeset.append(probeset[1]) normalized_probeset.append(probeset[2]) normalized_probeset.append(probeset[3]) normalized_probeset.append(probeset[4]) normalized_probeset.append(probeset[5]) normalized_probeset.append(probeset[6]) # normalized_probeset.append(probesetxref[1]) normalized_probeset.append(probesetxref[2]) # locus = probesetxref[3] geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus) normalized_probeset.append(geno[2]) normalized_probeset.append(geno[3]) # normalized_probesets.append(normalized_probeset) return normalized_probesets
def bxd_givenprobesetfreezes(probesetfreezesfile): file = open(probesetfreezesfile, 'r') for line in file: line = line.strip() cells = line.split() probesetfreezeid = cells[0] probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) probesetfreezename = probesetfreeze[1] probesetfreezefullname = probesetfreeze[2] probesetxrefs = probesets.get_probesetxref(probesetfreezeid) print "%s\t%s\t%s\t%d" % (probesetfreezeid, probesetfreezename, probesetfreezefullname, len(probesetxrefs)) file.close()
def generate_probesets(probesetfreezesfile, outputdir): file = open(probesetfreezesfile, 'r') for line in file: line = line.strip() cells = line.split() probesetfreezeid = cells[0] probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) probesetfreezeid = probesetfreeze[0] probesetfreezename = probesetfreeze[1] inbredset = datastructure.get_inbredset(probesetfreezeid) inbredsetid = inbredset[0] strains = datastructure.get_strains(inbredsetid) # outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+") outputfile.write("%s\t" % "ProbeSet Id") outputfile.write("%s\t" % "ProbeSet Name") outputfile.write('\t'.join([strain[1].upper() for strain in strains])) outputfile.write("\n") outputfile.flush() # probesetxrefs = probesets.get_probesetxref(probesetfreezeid) print probesetfreeze print 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]) # outputfile.write("%s\t" % probesetid) outputfile.write("%s\t" % probesetname) # for strain in strains: strainname = strain[1] strainname = strainname.lower() if strainname in probesetdata: value = probesetdata[strainname] else: value = 'x' outputfile.write("%s\t" % value) outputfile.write("\n") outputfile.flush() # outputfile.close() file.close()
def bxd_correlations_givenprobesetfreezes(probesetfreezesfile, outputdir): # inbredsetid = 1 genofile = "/home/leiyan/gn/web/genotypes/BXD.geno" # 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()
def generate_probesets(probesetfreezesfile, outputdir): file = open(probesetfreezesfile, 'r') for line in file: line = line.strip() cells = line.split() probesetfreezeid = cells[0] probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) probesetfreezeid = probesetfreeze[0] probesetfreezename = probesetfreeze[1] # outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+") outputfile.write("%s\t" % "ProbeSetId") outputfile.write("%s\t" % "ProbeSetName") outputfile.write("%s\t" % "Symbol") outputfile.write("%s\t" % "StrainNumbers") outputfile.write("\n") outputfile.flush() # probesetxrefs = probesets.get_probesetxref(probesetfreezeid) print probesetfreeze print len(probesetxrefs) for probesetxref in probesetxrefs: probesetid = probesetxref[0] probesetdataid = probesetxref[1] probeset = probesets.get_probeset(probesetid) probesetname = probeset[1] probesetsymbol = probeset[2] probesetdescription = probeset[3] probesetchr = probeset[5] probesetmb = probeset[6] probesetdata = probesets.get_probesetdata(probesetdataid) # outputfile.write("%s\t" % probesetid) outputfile.write("%s\t" % probesetname) outputfile.write("%s\t" % probesetsymbol) outputfile.write("%d" % len(probesetdata)) outputfile.write("\n") outputfile.flush() # outputfile.close() file.close()
def generate_probesets_2(probesetfreezesfile, outputdir): file = open(probesetfreezesfile, 'r') for line in file: line = line.strip() cells = line.split() probesetfreezeid = cells[0] probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) probesetfreezeid = probesetfreeze[0] probesetfreezename = probesetfreeze[1] inbredset = datastructure.get_inbredset(probesetfreezeid) inbredsetid = inbredset[0] # outputfile = open("%s/%d_%s.txt" % (outputdir, probesetfreezeid, probesetfreezename), "w+") outputfile.write("%s\t" % "ProbeSetId") outputfile.write("%s\t" % "Symbol") outputfile.write("%s\t" % "Description") outputfile.write("%s\t" % "Chr") outputfile.write("%s\t" % "MB") outputfile.write("%s\t" % "Marker_Chr") outputfile.write("%s\t" % "Marker_MB") outputfile.write("%s\t" % "Mean_Expression") outputfile.write("%s\t" % "SE") outputfile.write("%s\t" % "LRS") outputfile.write("%s\t" % "pValue") outputfile.write("\n") outputfile.flush() # probesetxrefs = probesets.get_probesetxref(probesetfreezeid) print("%s:\n\t%d probesetxrefs" % (probesetfreeze, len(probesetxrefs))) for probesetxref in probesetxrefs: # probesetid = probesetxref[0] locus = probesetxref[2] lrs = probesetxref[3] pvalue = probesetxref[4] mean = probesetxref[5] se = probesetxref[6] # probeset = probesets.get_probeset(probesetid) probesetname = probeset[1] probesetsymbol = probeset[2] probesetdescription = probeset[3] probesetchr = probeset[5] probesetmb = probeset[6] # if locus is None or not locus: genochr = "" genomb = "" else: geno = genotypes.get_geno(inbredsetid=inbredsetid, name=locus) genochr = geno[2] genomb = geno[3] # outputfile.write("%s\t" % probesetname) outputfile.write("%s\t" % probesetsymbol) outputfile.write("%s\t" % probesetdescription) outputfile.write("%s\t" % probesetchr) outputfile.write("%s\t" % probesetmb) outputfile.write("%s\t" % genochr) outputfile.write("%s\t" % genomb) outputfile.write("%s\t" % mean) outputfile.write("%s\t" % se) outputfile.write("%s\t" % lrs) outputfile.write("%s\t" % pvalue) outputfile.write("\n") outputfile.flush() # outputfile.close() file.close()