def format(self, conf=None):
p_3_letter, p_term_asterisk = self._format_config_aa(conf)
st_length = self.length or ""
if p_3_letter:
if p_term_asterisk:
s = "{alt}fs*{length}".format(alt=aa1_to_aa3(self.alt), length=st_length)
else:
s = "{alt}fsTer{length}".format(alt=aa1_to_aa3(self.alt), length=st_length)
else:
s = "{alt}fs*{length}".format(alt=self.alt, length=st_length)
return "(" + s + ")" if self.uncertain else s
def format(self, conf=None):
if self.ref is None and self.alt is None:
# raise HGVSError("RefAlt: ref and alt sequences are both undefined")
return "="
p_3_letter, p_term_asterisk, p_init_met = self._format_config_aa(conf)
if self.init_met and p_init_met:
s = "Met1?"
elif self.init_met and not p_init_met:
s = "?"
# subst and delins
elif self.ref is not None and self.alt is not None:
if self.ref == self.alt:
if p_3_letter:
s = "{ref}=".format(ref=aa1_to_aa3(self.ref))
if p_term_asterisk and s == "Ter=":
s = "*="
else:
s = "{ref}=".format(ref=self.ref)
elif len(self.ref) == 1 and len(self.alt) == 1:
if p_3_letter:
s = aa1_to_aa3(self.alt)
if p_term_asterisk and s == "Ter":
s = "*"
else:
s = self.alt
else:
if p_3_letter:
s = "delins{alt}".format(alt=aa1_to_aa3(self.alt))
if p_term_asterisk and s == "delinsTer":
s = "delins*"
else:
s = "delins{alt}".format(alt=self.alt)
# del case
elif self.ref is not None and self.alt is None:
s = "del"
# ins case
elif self.ref is None and self.alt is not None:
if p_3_letter:
s = "ins{alt}".format(alt=aa1_to_aa3(self.alt))
if p_term_asterisk and s == "insTer":
s = "ins*"
else:
s = "ins{alt}".format(alt=self.alt)
else:
raise RuntimeError("Should not be here")
return "(" + s + ")" if self.uncertain else s
def format(self, conf=None):
p_3_letter, p_term_asterisk = self._format_config_aa(conf)
st_alt = self.alt or ""
st_aaterm = self.aaterm or ""
st_length = self.length or ""
if p_3_letter:
st_alt = aa1_to_aa3(st_alt)
st_aaterm = aa1_to_aa3(st_aaterm)
if p_term_asterisk and st_alt == "Ter":
st_alt = "*"
if p_term_asterisk and st_aaterm == "Ter":
st_aaterm = "*"
s = "{alt}ext{term}{length}".format(alt=st_alt, term=st_aaterm, length=st_length)
return "(" + s + ")" if self.uncertain else s
def format(self, conf=None):
p_3_letter, p_term_asterisk = self._format_config(conf)
if p_3_letter:
s = aa1_to_aa3(self.alt) if self.alt != "?" else self.alt
if p_term_asterisk and s == "Ter":
s = "*"
else:
s = self.alt
return "(" + s + ")" if self.uncertain else s
def format(self, conf=None):
self.validate()
p_3_letter = hgvs.global_config.formatting.p_3_letter
p_term_asterisk = hgvs.global_config.formatting.p_term_asterisk
if conf and "p_3_letter" in conf and conf["p_3_letter"] is not None:
p_3_letter = conf["p_3_letter"]
if conf and "p_term_asterisk" in conf and conf["p_term_asterisk"] is not None:
p_term_asterisk = conf["p_term_asterisk"]
pos = "?" if self.base is None else str(self.base)
if p_3_letter:
aa = "?" if self.aa is None else aa1_to_aa3(self.aa)
if p_term_asterisk and aa == "Ter":
aa = "*"
else:
aa = "?" if self.aa is None else self.aa
s = aa + pos
return "(" + s + ")" if self.uncertain else s
def __str__(self):
self.validate()
pos = '?' if self.base is None else str(self.base)
aa = '?' if self.aa is None else aa1_to_aa3(self.aa)
s = aa + pos
return '('+s+')' if self.uncertain else s