def oligo_dg_vdisp(dg=None, *tags, **attrs): if dg is None: klass = UNKNOWN elif dg == 0: klass = OK else: klass = WARN return recursive_class_tag(tags, sig2(dg) if dg is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
def amplicon_dg_vdisp(dg=None, *tags, **attrs): if dg is None: klass = UNKNOWN elif dg >= -2: klass = OK elif dg >= -4 and dg < -2: klass = WARN else: klass = UHOH return recursive_class_tag(tags, sig2(dg) if dg is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
def amplicon_length_vdisp(length=None, *tags, **attrs): if not length: klass = UNKNOWN elif length < 120: klass = OK elif length >= 120 and length < 150: klass = WARN else: klass = UHOH return recursive_class_tag(tags, str(length) if length else 'Unknown', **__merge_class_attrs(klass, **attrs))
def gc_content_vdisp(gc=None, *tags, **attrs): if gc is None: klass = UNKNOWN if gc >= 40 and gc <= 60: klass = OK elif (gc >= 35 and gc < 40) or (gc > 60 and gc <= 65): klass = WARN else: klass = UHOH return recursive_class_tag(tags, "%s%%" % sig0(gc) if gc is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
def intra_primer_delta_tm_vdisp(fp_tm=None, rp_tm=None, *tags, **attrs): if not fp_tm or not rp_tm: klass = UNKNOWN diff = None else: diff = abs(rp_tm-fp_tm) if abs(rp_tm-fp_tm) < 2: klass = OK else: klass = WARN return recursive_class_tag(tags, sig1(diff) if diff is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
def primer_tm_vdisp(tm=None, *tags, **attrs): if not tm: klass = UNKNOWN elif tm >= 58.95 and tm < 63.05: klass = OK elif (tm > 55 and tm < 58.95) or tm >= 63.05: klass = WARN else: klass = UHOH return recursive_class_tag(tags, sig1(tm) if tm else 'Unknown', **__merge_class_attrs(klass, **attrs))
def probe_tm_vdisp(tm=None, *tags, **attrs):
if attrs.pop('snp', False):
max_tm = 68.05
else:
max_tm = 70.05
if not tm:
klass = UNKNOWN
elif tm >= 64.95 and tm < max_tm:
klass = OK
else:
klass = WARN
return recursive_class_tag(tags, sig1(tm) if tm else 'Unknown', **__merge_class_attrs(klass, **attrs))
def primer_probe_delta_tm_vdisp(primer_tm=None, probe_tm=None, *tags, **attrs): if not primer_tm or not probe_tm: klass = UNKNOWN diff = None else: diff = probe_tm-primer_tm if diff > 1: klass = OK elif diff > 0: klass = WARN else: klass = UHOH return recursive_class_tag(tags, sig1(diff) if diff is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
def max_overlap_vdisp(overlap=None, *tags, **attrs): """ Assumes output comes from max_overlap function (len, (off, off)) """ if overlap is None: klass = UNKNOWN elif overlap[0] < 6: klass = OK elif overlap[0] < 8: klass = WARN else: klass = UHOH return recursive_class_tag(tags, str(overlap[0]) if overlap is not None else 'Unknown', **__merge_class_attrs(klass, **attrs))
