def call_annotation_variant(annotation_file, ref_aligned, seq_aligned, ref_positions, seq_positions, sequence_id = 666):
table = CodonTable.ambiguous_dna_by_id[1]
list_annotations = []
class Ann:
def __init__(self, ann_type, ann_pos, gene, protein, protein_id, aa_seq):
self.ann_type = ann_type
self.ann_pos = ann_pos
self.gene = gene
self.protein = protein
self.protein_id = protein_id
self.aa_seq = aa_seq
def parse_pos(l):
return [(int(pos.strip().split(",")[0]), int(pos.strip().split(",")[1])) for pos in l.strip().split(";")]
ref_annotations = []
with open(annotation_file) as f:
for line in f:
s = line.strip().split("\t")
ann_type = s[2]
ann_pos = parse_pos(s[3])
gene = None if s[4] == "." else s[4]
protein = None if s[5] == "." else s[5]
protein_id = None if s[6] == "." else s[6]
aa_seq = None if s[7] == "." else s[7]
ref_annotations.append(Ann(ann_type, ann_pos, gene, protein, protein_id, aa_seq))
proteins_not_multiple_of_3 = []
for annotation in ref_annotations:
gene = annotation.gene
protein = annotation.protein
protein_id = annotation.protein_id
atype = annotation.ann_type
nuc_start = annotation.ann_pos[0][0]
nuc_stop = annotation.ann_pos[-1][1]
# get the nucleotide sequence
nuc_seq = "".join(
[x[1] for x in zip(ref_positions, seq_aligned) if nuc_start <= x[0] <= nuc_stop]).replace("-", "")
list_mutations = []
if annotation.ann_type == 'mature_protein_region' or annotation.ann_type == 'CDS':
# dna_ref is the concatenation of the nucleotides of the aligned seq within the range(s) of this protein
# with gaps deleted. This string is what is translated in the cell for this protein.
dna_ref = ''
for (start, stop) in annotation.ann_pos:
dna_ref += "".join([x[1] for x in zip(ref_positions, seq_aligned) if start <= x[0] <= stop]).replace("-", "")
if len(dna_ref) % 3 == 0 and len(dna_ref) > 0:
aa_seq_with_symbols = Seq._translate_str(dna_ref, table, cds=False)
# symbols e.g. * that means Ter
aa_seq = aa_seq_with_symbols.replace("*", "")
# annotation.aa_seq is the reference AA sequence from the annotation files for this protein
alignment_aa = pairwise2.align.globalms(annotation.aa_seq, aa_seq, 3, -1, -3, -1)
try:
ref_aligned_aa = alignment_aa[0][0]
seq_aligned_aa = alignment_aa[0][1]
except IndexError:
continue
ref_positions_aa = np.zeros(len(seq_aligned_aa), dtype=int)
pos = 0
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] != '-':
pos += 1
ref_positions_aa[i] = pos
seq_positions_aa = np.zeros(len(seq_aligned_aa), dtype=int)
pos = 0
for i in range(len(ref_aligned_aa)):
if seq_aligned_aa[i] != '-':
pos += 1
seq_positions_aa[i] = pos
list_mutations = []
ins_open = False
ins_len = 0
ins_pos = None
ins_seq = ""
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] == '-':
ins_open = True
ins_len += 1
ins_pos = ref_positions_aa[i]
ins_seq += seq_aligned_aa[i]
else:
if ins_open:
v = (gene, protein, protein_id, ins_pos, "-" * ins_len, ins_seq, "INS")
list_mutations.append(v)
ins_open = False
ins_len = 0
ins_pos = None
ins_seq = ""
if ins_open:
v = (gene, protein, protein_id, ins_pos, "-" * ins_len, ins_seq, "INS")
list_mutations.append(v)
del_open = False
del_len = 0
del_pos = None
del_seq = ""
for i in range(len(ref_aligned_aa)):
if seq_aligned_aa[i] == '-':
if not del_open:
del_pos = ref_positions_aa[i]
del_pos_seq = seq_positions_aa[i]
del_open = True
del_len += 1
del_seq += ref_aligned_aa[i]
else:
if del_open:
v = (gene, protein, protein_id, del_pos, del_seq, "-" * del_len, "DEL")
list_mutations.append(v)
del_open = False
del_len = 0
del_pos = None
del_pos_seq = None
del_seq = ""
if del_open:
v = (gene, protein, protein_id, del_pos, del_seq, "-" * del_len, "DEL")
list_mutations.append(v)
mut_open = False
mut_len = 0
mut_pos = None
mut_pos_seq = None
mut_seq_original = ""
mut_seq_mutated = ""
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] != '-' and seq_aligned_aa[i] != '-' and ref_aligned_aa[i] != seq_aligned_aa[i]:
if not mut_open:
mut_pos = ref_positions_aa[i]
mut_pos_seq = seq_positions_aa[i]
mut_open = True
mut_len += 1
mut_seq_original += ref_aligned_aa[i]
mut_seq_mutated += seq_aligned_aa[i]
else:
if mut_open:
v = (gene, protein, protein_id, mut_pos, mut_seq_original, mut_seq_mutated, "SUB")
list_mutations.append(v)
mut_open = False
mut_len = 0
mut_pos = None
mut_pos_seq = None
mut_seq_original = ""
mut_seq_mutated = ""
if mut_open:
v = (gene, protein, protein_id, mut_pos, mut_seq_original, mut_seq_mutated, "SUB")
list_mutations.append(v)
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, nuc_seq, aa_seq, list_mutations))
elif len(dna_ref) == 0:
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, None, None, []))
else: # nucleotide sequence not multiple of 3
proteins_not_multiple_of_3.append(protein)
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, nuc_seq, None, []))
elif atype == 'gene':
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, nuc_seq, None, []))
# log frameshift not detectable in the final output
if len(proteins_not_multiple_of_3) > 0:
logger.warning(f"sequence ID {sequence_id} has proteins of length not multiple of 3 {proteins_not_multiple_of_3}")
return list_annotations
def call_annotation_variant(annotation_file, ref_aligned, seq_aligned, ref_positions, seq_positions, sequence_id = 666):
table = CodonTable.ambiguous_dna_by_id[1]
list_annotations = []
class Ann:
def __init__(self, ann_type, ann_pos, gene, protein, protein_id, aa_seq):
self.ann_type = ann_type
self.ann_pos = ann_pos
self.gene = gene
self.protein = protein
self.protein_id = protein_id
self.aa_seq = aa_seq
def parse_pos(l):
return [(int(pos.strip().split(",")[0]), int(pos.strip().split(",")[1])) for pos in l.strip().split(";")]
ref_annotations = []
with open(annotation_file) as f:
for line in f:
s = line.strip().split("\t")
ann_type = s[2]
ann_pos = parse_pos(s[3])
gene = None if s[4] == "." else s[4]
protein = None if s[5] == "." else s[5]
protein_id = None if s[6] == "." else s[6]
aa_seq = None if s[7] == "." else s[7]
ref_annotations.append(Ann(ann_type, ann_pos, gene, protein, protein_id, aa_seq))
for annotation in ref_annotations:
gene = annotation.gene
protein = annotation.protein
protein_id = annotation.protein_id
atype = annotation.ann_type
nuc_start = annotation.ann_pos[0][0]
nuc_stop = annotation.ann_pos[-1][1]
nuc_seq = "".join(
[x[1] for x in zip(ref_positions, seq_aligned) if nuc_start <= x[0] and nuc_stop >= x[0]]).replace("-", "")
#if nuc_seq is not None and aa_seq is None:
# logger.warning('nuc_seq is not None and aa_seq is None (' + gene + ',' + protein + ')')
list_mutations = []
if annotation.ann_type == 'mature_protein_region' or annotation.ann_type == 'CDS':
dna_ref = ''
for (start, stop) in annotation.ann_pos:
dna_ref += "".join([x[1] for x in zip(ref_positions, seq_aligned) if start <= x[0] and stop >= x[0]]).replace("-", "")
if len(dna_ref)%3 == 0 and len(dna_ref) > 0:
aa_seq = Seq._translate_str(dna_ref, table, cds=False).replace("*", "")
alignment_aa = pairwise2.align.globalms(annotation.aa_seq, aa_seq, 3, -1, -3, -1)
try:
ref_aligned_aa = alignment_aa[0][0]
seq_aligned_aa = alignment_aa[0][1]
except IndexError:
continue
ref_positions_aa = np.zeros(len(seq_aligned_aa), dtype=int)
pos = 0
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] != '-':
pos += 1
ref_positions_aa[i] = pos
seq_positions_aa = np.zeros(len(seq_aligned_aa), dtype=int)
pos = 0
for i in range(len(ref_aligned_aa)):
if seq_aligned_aa[i] != '-':
pos += 1
seq_positions_aa[i] = pos
list_mutations = []
ins_open = False
ins_len = 0
ins_pos = None
ins_seq = ""
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] == '-':
ins_open = True
ins_len += 1
ins_pos = ref_positions_aa[i]
ins_seq += seq_aligned_aa[i]
else:
if ins_open:
v = (gene, protein, protein_id, ins_pos, "-" * ins_len, ins_seq, "INS")
list_mutations.append(v)
ins_open = False
ins_len = 0
ins_pos = None
ins_seq = ""
if ins_open:
v = (gene, protein, protein_id, ins_pos, "-" * ins_len, ins_seq, "INS")
list_mutations.append(v)
del_open = False
del_len = 0
del_pos = None
del_seq = ""
for i in range(len(ref_aligned_aa)):
if seq_aligned_aa[i] == '-':
if not del_open:
del_pos = ref_positions_aa[i]
del_pos_seq = seq_positions_aa[i]
del_open = True
del_len += 1
del_seq += ref_aligned_aa[i]
else:
if del_open:
v = (gene, protein, protein_id, del_pos, del_seq, "-" * del_len, "DEL")
list_mutations.append(v)
del_open = False
del_len = 0
del_pos = None
del_pos_seq = None
del_seq = ""
if del_open:
v = (gene, protein, protein_id, del_pos, del_seq, "-" * del_len, "DEL")
list_mutations.append(v)
mut_open = False
mut_len = 0
mut_pos = None
mut_pos_seq = None
mut_seq_original = ""
mut_seq_mutated = ""
for i in range(len(ref_aligned_aa)):
if ref_aligned_aa[i] != '-' and seq_aligned_aa[i] != '-' and ref_aligned_aa[i] != seq_aligned_aa[i]:
if not mut_open:
mut_pos = ref_positions_aa[i]
mut_pos_seq = seq_positions_aa[i]
mut_open = True
mut_len += 1
mut_seq_original += ref_aligned_aa[i]
mut_seq_mutated += seq_aligned_aa[i]
else:
if mut_open:
v = (gene, protein, protein_id, mut_pos, mut_seq_original, mut_seq_mutated, "SUB")
list_mutations.append(v)
mut_open = False
mut_len = 0
mut_pos = None
mut_pos_seq = None
mut_seq_original = ""
mut_seq_mutated = ""
if mut_open:
v = (gene, protein, protein_id, mut_pos, mut_seq_original, mut_seq_mutated, "SUB")
list_mutations.append(v)
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, nuc_seq, aa_seq, list_mutations))
elif len(dna_ref) == 0:
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, None, None, []))
else:
list_annotations.append(
(gene, protein, protein_id, atype, nuc_start, nuc_stop, nuc_seq, None, []))
return list_annotations
