def create_maf_distribution(
seqs, distrib_fhand=None, plot_fhand=None, summary_fhand=None, groups=None, group_kind=None
):
"It creates the distribution of the maf (not takes in account ref allele)"
title = "maf"
if groups and group_kind:
title = "maf (%s: %s)" % (group_kind, ",".join(groups))
mafs = CachedArray("f")
for seq in seqs:
for snv in seq.get_features("snv"):
maf = calculate_maf_frequency(snv, groups=groups, group_kind=group_kind)
if maf:
mafs.append(maf)
if list(mafs):
create_distribution(
mafs,
labels={"title": title},
distrib_fhand=distrib_fhand,
bins=None,
plot_fhand=plot_fhand,
range_=None,
summary_fhand=summary_fhand,
calculate_freqs=False,
remove_outliers=False,
)
def write(self, sequence, selected_snv_location):
'It writes a seq with the alternative alleles in one position and Ns in the others.'
start = selected_snv_location - self._length
end = selected_snv_location + self._length + 1
if start < 0:
start = 0
if end > len(sequence):
end = len(sequence)
sequence = sequence[start: end]
selected_snv_location -= start
maf_threshold = self._maf
prev_seq_end = 0
seq_to_print = ''
for snv in sequence.get_features(kind='snv'):
# snv start and end [start, end[.
# Correcting the previous sequence slice
snv_start = snv.location.start.position - start
snv_end = snv.location.end.position - start
# join the previous sequence to the sequence to print
seq_to_print += str(sequence[prev_seq_end:snv_start].seq)
prev_seq_end = snv_end
if snv_start == selected_snv_location:
#subtituir por allelos
snv_kind = calculate_snv_kind(snv)
if snv_kind != SNP:
msg = "We don't know how to print anything but SNPs"
raise NotImplementedError(msg)
alleles = '/'.join([a[0] for a in snv.qualifiers['alleles'].keys()])
to_print = '[{0:s}]'.format(alleles)
else:
if maf_threshold is not None:
snv_maf = calculate_maf_frequency(snv)
write_abundant_allele = True if snv_maf > maf_threshold else False
else:
write_abundant_allele = False
if write_abundant_allele:
# most abundant allele
to_print = _get_major_allele(snv)
else:
# Ns
snv_kind = calculate_snv_kind(snv)
if snv_kind == SNP:
to_print = _snp_to_iupac(snv, sequence)
elif snv_kind in (DELETION, COMPLEX, INDEL):
ref_allele = snv.qualifiers['reference_allele']
to_print = ref_allele[0] + 'N' * (len(ref_allele) - 1)
else:
to_print = 'N'
seq_to_print += to_print
else:
seq_to_print += str(sequence[prev_seq_end:end + 1].seq)
name = sequence.name + '_' + str(selected_snv_location + 1)
self.fhand.write('>%s\n%s\n' % (name, seq_to_print))
self.fhand.flush()
def calculate_mafs_group(seqs, groups=None, group_kind=None):
'It calculates the snv heterozygosity of a given group'
maf_profile = {}
for seq in seqs:
for snv in seq.get_features('snv'):
maf = calculate_maf_frequency(snv, group_kind=group_kind,
groups=groups)
if maf is not None:
location = snv.location.start.position
seq_name = seq.name
if seq_name not in maf_profile:
maf_profile[seq_name] = []
maf_profile[seq_name].append((location, maf))
return maf_profile
def major_allele_freq_filter(sequence):
'The filter'
if sequence is None:
return None
for snv in sequence.get_features(kind='snv'):
previous_result = _get_filter_result(snv, 'maf',
threshold=parameters)
if previous_result is not None:
continue
maf = calculate_maf_frequency(snv, groups=groups,
group_kind=group_kind)
if maf > frequency or maf is None:
result = True
else:
result = False
_add_filter_result(snv, 'maf', result, threshold=parameters)
return sequence
def _snv_to_n(snv, sequence, position, maf=None):
'It returns the n for each snp'
genotype = []
for allele, kind in snv.qualifiers['alleles'].keys():
if kind == SNP and not genotype:
snv_maf = calculate_maf_frequency(snv)
if maf and snv_maf > maf:
genotype = [_get_major_allele(snv)]
else:
snp_iupac = _snp_to_iupac(snv, sequence)
genotype = [snp_iupac]
elif kind == DELETION:
len_del = len(allele)
genotype.extend(['N'] * (len_del - len(genotype)))
elif kind == INSERTION:
geno = sequence[position] + len(allele) * 'N'
if genotype:
genotype[0] = geno
else:
genotype.append(geno)
return genotype
