def __fill_cD(self, iL=None, snpL=None):
"""Fill *self.cF*.
Fill *self.cF* with data from reference at chromosome
*self.chrom* and position *self.pos*. Possible SNPs in
*self.vcfL* at this position are considered.
:param [int] iL: List with vcf indices of the SNPs in *snpL*,
must be sorted.
:param [NucBase] snpL: List with :class:`NucBase
<cflib.vcf.NucBase>` SNPs at this position. None, if
there is no SNP.
:raises: :class:`NotAValidRefBase
<cflib.seqbase.NotAValidRefBase>`,
:class:`SequenceDataError
<cflib.seqbase.SequenceDataError>`
:class:`NotAValidRefBae <cflib.seqbase.NotAValidRefBase>` is
raised if the reference base is not valid (e.g. N).
:class:`SequenceDataError <cflib.seqbase.SequenceDataError>`
is raised if the chromosome names do not match.
"""
if snpL is not None:
logging.debug("Next SNP(s):")
for s in snpL:
logging.debug(s.get_info())
def get_refBase():
"""Get reference base on *chrom* at *pos*."""
return self.refSeq.data[self.pos].lower()
def update_cD(pop, baseI, delta=self.ploidy):
"""Add counts to the countsDictionary cD."""
# FIXME: IUPAC code not handled here. Is this even necessary?
if baseI == dna['n'] or baseI == dna['*']:
logging.debug("Reference base is unknown. Continue.")
return
if pop in range(0, self.nPop):
self.cD[pop][baseI] += delta
logging.debug(
"Updating counts dictionary; population %s, "
"base index %s.", pop, baseI)
else:
logging.info(
"Ignoring data because population index %s is "
"out of range.", pop)
raise ValueError()
self.purge_cD()
# If we check for synonymous bases, do not do anything if base
# is not 4-fold degenerate.
if self.onlySynonymous is True:
if self.refSeq.is_synonymous(self.pos) is False:
logging.debug(
"Rejection; %s at position %s "
"is not a synonymous base.", self.refSeq.data[self.pos],
self.pos)
raise NoSynBase()
refBase = get_refBase()
try:
r = dna[refBase]
except KeyError:
raise sb.NotAValidRefBase()
# If there are no SNPS, fill *self.cD* with data from reference.
if iL is None:
for i in range(self.nV):
for pop in self.assM[i]:
update_cD(pop, r)
elif (snpL is not None) and (len(iL) == len(snpL)):
# Else, only fill *self.cD* where the individual has no SNP.
for i in range(self.nV):
if i not in iL:
for pop in self.assM[i]:
update_cD(pop, r)
# Now traverse the SNPs.
for sI in range(len(iL)):
# Check if the reference bases match.
vcfRefBase = snpL[sI].get_ref_base().lower()
# Thu Jun 9 09:26:55 CEST 2016: Just use first base if
# there are more.
indel = False
if len(vcfRefBase) > 1:
logging.warn("Indel at chrom %s pos %d.", self.chrom,
self.pos + self.offset)
indel = True
vcfRefBase = vcfRefBase[0]
if dna[vcfRefBase] != r:
print("Error at NucBase:")
snpL[sI].print_info()
print("The reference base at position",
self.pos,
"on chromosome",
self.chrom,
"is",
refBase,
end=".\n")
print("The reference base of the VCF file is",
vcfRefBase,
end=".\n")
raise sb.SequenceDataError("Reference bases do not match.")
altBases = snpL[sI].get_alt_base_list()
for altBase in altBases:
if len(altBase) > 1:
indel = True
logging.warn("Indel at chrom %s pos %d.", self.chrom,
self.pos + self.offset)
spData = snpL[sI].get_speciesData()
vI = iL[sI]
# Loop over individuals.
for i in range(0, len(spData)):
# Loop over chromatides (e.g. diploid).
for d in range(0, self.ploidy):
if spData[i][d] is None:
pass
elif indel or spData[i][d] == 0:
bI = r
update_cD(self.assM[vI][i], bI, delta=1)
else:
bI = dna[altBases[spData[i][d] - 1]]
logging.debug("Use SNP of %s, population %s",
self.indM[vI][i], self.assM[vI][i])
update_cD(self.assM[vI][i], bI, delta=1)
else:
raise sb.SequenceDataError("SNP information is not correct.")
def add_base_to_sequence(self,
pop_id,
base_char,
double_fixed_sites=False):
"""Adds the base given in `base_char` to the counts of population with
id `pop_id`. If `double_fixed_sited` is true, fixed sites are
counted twice. This makes sense, when heterozygotes are
encoded with IUPAC codes.
"""
base = base_char.lower()
try:
base_id = dna[base]
except KeyError:
raise sb.NotAValidRefBase()
# Honor IUPAC code.
if base_id <= 3:
self.cD[pop_id][base_id] += 1
if double_fixed_sites:
self.cD[pop_id][base_id] += 1
return
elif base == 'r':
# C or G.
self.cD[pop_id][0] += 1
self.cD[pop_id][2] += 1
elif base == 'y':
# C or T.
self.cD[pop_id][1] += 1
self.cD[pop_id][3] += 1
elif base == 's':
# G or C.
self.cD[pop_id][1] += 1
self.cD[pop_id][2] += 1
elif base == 'w':
# A or T.
self.cD[pop_id][0] += 1
self.cD[pop_id][3] += 1
elif base == 'k':
# G or T.
self.cD[pop_id][2] += 1
self.cD[pop_id][3] += 1
elif base == 'm':
# A or C.
self.cD[pop_id][0] += 1
self.cD[pop_id][1] += 1
elif base == 'b':
# C or G or T.
logging.info("Ambivalent base with 3 possibilities.")
logging.info("This base will be ignored upon running PoMo.")
self.cD[pop_id][1] += 1
self.cD[pop_id][2] += 1
self.cD[pop_id][3] += 1
elif base == 'd':
# A or G or T.
logging.info("Ambivalent base with 3 possibilities.")
logging.info("This base will be ignored upon running PoMo.")
self.cD[pop_id][0] += 1
self.cD[pop_id][2] += 1
self.cD[pop_id][3] += 1
elif base == 'h':
# A or C or T.
logging.info("Ambivalent base with 3 possibilities.")
logging.info("This base will be ignored upon running PoMo.")
self.cD[pop_id][0] += 1
self.cD[pop_id][1] += 1
self.cD[pop_id][3] += 1
elif base == 'v':
# A or C or G.
logging.info("Ambivalent base with 3 possibilities.")
logging.info("This base will be ignored upon running PoMo.")
self.cD[pop_id][0] += 1
self.cD[pop_id][1] += 1
self.cD[pop_id][2] += 1
elif base == 'n':
# Any base.
pass
elif base == '-' or base == '.':
# Gap.
pass
logging.info("IUPAC code handled. This might bias the analysis.")
return