[ArmedXpert Plugin] Get OSIRIS allele fit for all alleles

osiris_allele_fit.py

src = Sources[0]

src.OpenOriginalDocument()
try:
    for sample in src.AllEntries:
        for locus in sample.Loci:
            for allele in locus.Alleles:
                peak_name = str(allele.Name)
                if peak_name.endswith(' OL'):
                    peak_name = peak_name.replace(' OL', '')
                if 'amel' in allele.Locus.lower():
                    # OSIRIS Amelogenin alleles are numbered, X=1, Y=2
                    peak_name = {'x': 1, 'y': 2}.get(allele.Name.lower(), '')
                fit = src.GetSampleElementValue(
                    sample,
                    "Locus[LocusName='%s']/Allele[Name='%s']/Fit" % (
                        allele.Locus,
                        peak_name
                    )
                )
                if fit is None:
                    
                    artifact_fit = src.GetSampleElementValue(
                        sample,
                        'ChannelAlerts/Channel/Artifact/Allele[Locus="%s"][Name="%s"]/../Fit' % (
                            allele.Locus,
                            peak_name
                        )
                    )
                print 'Sample %s, Locus %s, Allele %s, Fit %s' % (
                    sample.SampleName, locus.Identifier, allele.Name, fit
                )
finally:
    src.CloseOriginalDocument()