def c_to_n(self, c_interval):
"""convert a transcript CDS (c.) interval to a transcript cDNA (n.) interval"""
if self.cds_start_i is None: # cds_start_i defined iff cds_end_i defined; see assertion above
raise HGVSUsageError(
"CDS is undefined for {self.tx_ac}; cannot map from c. coordinate (non-coding transcript?)".format(
self=self))
# start
if c_interval.start.datum == hgvs.location.CDS_START and c_interval.start.base < 0:
rs = c_interval.start.base + self.cds_start_i + 1
elif c_interval.start.datum == hgvs.location.CDS_START and c_interval.start.base > 0:
rs = c_interval.start.base + self.cds_start_i
elif c_interval.start.datum == hgvs.location.CDS_END:
rs = c_interval.start.base + self.cds_end_i
# end
if c_interval.end.datum == hgvs.location.CDS_START and c_interval.end.base < 0:
re = c_interval.end.base + self.cds_start_i + 1
elif c_interval.end.datum == hgvs.location.CDS_START and c_interval.end.base > 0:
re = c_interval.end.base + self.cds_start_i
elif c_interval.end.datum == hgvs.location.CDS_END:
re = c_interval.end.base + self.cds_end_i
if rs <= 0 or re > self.tgt_len:
raise HGVSError("The given coordinate is outside the bounds of the reference sequence.")
n_interval = hgvs.location.BaseOffsetInterval(
start=hgvs.location.BaseOffsetPosition(
base=rs, offset=c_interval.start.offset, datum=hgvs.location.SEQ_START),
end=hgvs.location.BaseOffsetPosition(base=re, offset=c_interval.end.offset, datum=hgvs.location.SEQ_START),
uncertain=c_interval.uncertain)
return n_interval
def c_to_n(self, c_interval, strict_bounds=None):
"""convert a transcript CDS (c.) interval to a transcript cDNA (n.) interval"""
if strict_bounds is None:
strict_bounds = global_config.mapping.strict_bounds
if self.cds_start_i is None:
raise HGVSUsageError(
"CDS is undefined for {self.tx_ac}; this accession appears to be for a non-coding transcript"
.format(self=self))
def pos_c_to_n(pos):
if pos.datum == Datum.CDS_START:
n = pos.base + self.cds_start_i
if pos.base < 0: # correct for lack of c.0 coordinate
n += 1
elif pos.datum == Datum.CDS_END:
n = pos.base + self.cds_end_i
if n <= 0: # correct for lack of n.0 coordinate
n -= 1
if (n <= 0 or n > self.tgt_len):
if strict_bounds:
raise HGVSInvalidIntervalError(f"c.{pos} coordinate is out of bounds")
return hgvs.location.BaseOffsetPosition(base=n,
offset=pos.offset,
datum=Datum.SEQ_START)
n_start = pos_c_to_n(c_interval.start)
n_end = pos_c_to_n(c_interval.end)
n_interval = hgvs.location.BaseOffsetInterval(start=pos_c_to_n(c_interval.start),
end=pos_c_to_n(c_interval.end),
uncertain=c_interval.uncertain)
return n_interval
def n_to_c(self, n_interval, strict_bounds=None):
"""convert a transcript cDNA (n.) interval to a transcript CDS (c.) interval"""
if strict_bounds is None:
strict_bounds = global_config.mapping.strict_bounds
if self.cds_start_i is None: # cds_start_i defined iff cds_end_i defined; see assertion above
raise HGVSUsageError(
"CDS is undefined for {self.tx_ac}; cannot map to c. coordinate (non-coding transcript?)"
.format(self=self))
if strict_bounds and (n_interval.start.base <= 0 or n_interval.end.base > self.tgt_len):
raise HGVSInvalidIntervalError(
"The given coordinate is outside the bounds of the reference sequence.")
def pos_n_to_c(pos):
if pos.base <= self.cds_start_i:
c = pos.base - self.cds_start_i - (1 if pos.base > 0 else 0)
c_datum = Datum.CDS_START
elif pos.base > self.cds_start_i and pos.base <= self.cds_end_i:
c = pos.base - self.cds_start_i
c_datum = Datum.CDS_START
else:
c = pos.base - self.cds_end_i
c_datum = Datum.CDS_END
return hgvs.location.BaseOffsetPosition(base=c, offset=pos.offset, datum=c_datum)
c_interval = hgvs.location.BaseOffsetInterval(start=pos_n_to_c(n_interval.start),
end=pos_n_to_c(n_interval.end),
uncertain=n_interval.uncertain)
return c_interval
def c_to_n(self, c_interval, strict_bounds=None):
"""convert a transcript CDS (c.) interval to a transcript cDNA (n.) interval"""
if strict_bounds is None:
strict_bounds = global_config.mapping.strict_bounds
if self.cds_start_i is None: # cds_start_i defined iff cds_end_i defined; see assertion above
raise HGVSUsageError(
"CDS is undefined for {self.tx_ac}; cannot map from c. coordinate (non-coding transcript?)"
.format(self=self))
# start
if c_interval.start.datum == Datum.CDS_START and c_interval.start.base < 0:
n_start = c_interval.start.base + self.cds_start_i + 1
elif c_interval.start.datum == Datum.CDS_START and c_interval.start.base > 0:
n_start = c_interval.start.base + self.cds_start_i
elif c_interval.start.datum == Datum.CDS_END:
n_start = c_interval.start.base + self.cds_end_i
# end
if c_interval.end.datum == Datum.CDS_START and c_interval.end.base < 0:
n_end = c_interval.end.base + self.cds_start_i + 1
elif c_interval.end.datum == Datum.CDS_START and c_interval.end.base > 0:
n_end = c_interval.end.base + self.cds_start_i
elif c_interval.end.datum == Datum.CDS_END:
n_end = c_interval.end.base + self.cds_end_i
if strict_bounds and (n_start <= 0 or n_end > self.tgt_len):
raise HGVSInvalidIntervalError(
"The given coordinate is outside the bounds of the reference sequence."
)
n_interval = hgvs.location.BaseOffsetInterval(
start=hgvs.location.BaseOffsetPosition(
base=n_start,
offset=c_interval.start.offset,
datum=Datum.SEQ_START),
end=hgvs.location.BaseOffsetPosition(base=n_end,
offset=c_interval.end.offset,
datum=Datum.SEQ_START),
uncertain=c_interval.uncertain)
return n_interval
def n_to_c(self, n_interval):
"""convert a transcript cDNA (n.) interval to a transcript CDS (c.) interval"""
if self.cds_start_i is None: # cds_start_i defined iff cds_end_i defined; see assertion above
raise HGVSUsageError(
"CDS is undefined for {self.tx_ac}; cannot map to c. coordinate (non-coding transcript?)"
.format(self=self))
if n_interval.start.base <= 0 or n_interval.end.base > self.tgt_len:
raise HGVSError(
"The given coordinate is outside the bounds of the reference sequence."
)
# start
if n_interval.start.base <= self.cds_start_i:
cs = n_interval.start.base - (self.cds_start_i + 1)
cs_datum = Datum.CDS_START
elif n_interval.start.base > self.cds_start_i and n_interval.start.base <= self.cds_end_i:
cs = n_interval.start.base - self.cds_start_i
cs_datum = Datum.CDS_START
else:
cs = n_interval.start.base - self.cds_end_i
cs_datum = Datum.CDS_END
# end
if n_interval.end.base <= self.cds_start_i:
ce = n_interval.end.base - (self.cds_start_i + 1)
ce_datum = Datum.CDS_START
elif n_interval.end.base > self.cds_start_i and n_interval.end.base <= self.cds_end_i:
ce = n_interval.end.base - self.cds_start_i
ce_datum = Datum.CDS_START
else:
ce = n_interval.end.base - self.cds_end_i
ce_datum = Datum.CDS_END
c_interval = hgvs.location.BaseOffsetInterval(
start=hgvs.location.BaseOffsetPosition(
base=cs, offset=n_interval.start.offset, datum=cs_datum),
end=hgvs.location.BaseOffsetPosition(base=ce,
offset=n_interval.end.offset,
datum=ce_datum),
uncertain=n_interval.uncertain)
return c_interval