def sv_end(pos, alt, svend=None, svlen=None):
"""Return the end coordinate for a structural variant
The END field from INFO usually works fine, although for some cases like insertions the callers
set end to same as pos. In those cases we can hope that there is a svlen...
Translocations needs their own treatment as usual
Args:
pos(int)
alt(str)
svend(int)
svlen(int)
Returns:
end(int)
"""
end = svend
if ":" in alt:
match = BND_ALT_PATTERN.match(alt)
if match:
end = int(match.group(2))
if svend == pos:
if svlen:
end = pos + svlen
return end
def get_end_chrom(alt, chrom):
"""Return the end chromosome for a tranlocation
Args:
alt(str)
chrom(str)
Returns:
end_chrom(str)
"""
end_chrom = chrom
if ":" not in alt:
return end_chrom
match = BND_ALT_PATTERN.match(alt)
# BND will often be translocations between different chromosomes
if match:
other_chrom = match.group(1)
match = CHR_PATTERN.match(other_chrom)
end_chrom = match.group(2)
return end_chrom
def get_end(pos, alt, category, snvend=None, svend=None, svlen=None):
"""Return the end coordinate for a variant
Args:
pos(int)
alt(str)
category(str)
snvend(str)
svend(int)
svlen(int)
Returns:
end(int)
"""
# If nothing is known we set end to be same as start
end = pos
# If variant is snv or indel we know that cyvcf2 can handle end pos
if category in ('snv', 'indel', 'cancer'):
end = snvend
# With SVs we have to be a bit more careful
elif category == 'sv':
# The END field from INFO usually works fine
end = svend
# For some cases like insertions the callers set end to same as pos
# In those cases we can hope that there is a svlen...
if svend == pos:
if svlen:
end = pos + svlen
# If variant is 'BND' they have ':' in alt field
# Information about other end is in the alt field
if ':' in alt:
match = BND_ALT_PATTERN.match(alt)
if match:
end = int(match.group(2))
return end
def get_end(pos, alt, category, snvend=None, svend=None, svlen=None):
"""Return the end coordinate for a variant
Args:
pos(int)
alt(str)
category(str)
snvend(str)
svend(int)
svlen(int)
Returns:
end(int)
"""
# If nothing is known we set end to be same as start
end = pos
# If variant is snv or indel we know that cyvcf2 can handle end pos
if category in ('snv', 'indel', 'cancer'):
end = snvend
# With SVs we have to be a bit more careful
elif category == 'sv':
# The END field from INFO usually works fine
end = svend
# For some cases like insertions the callers set end to same as pos
# In those cases we can hope that there is a svlen...
if svend == pos:
if svlen:
end = pos + svlen
# If variant is 'BND' they have ':' in alt field
# Information about other end is in the alt field
if ':' in alt:
match = BND_ALT_PATTERN.match(alt)
if match:
end = int(match.group(2))
return end
def parse_coordinates(variant, category):
"""Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>,
'sub_category':<str>,
'mate_id':<str>,
'cytoband_start':<str>,
'cytoband_end':<str>,
}
"""
ref = variant.REF
alt = variant.ALT[0]
chrom_match = CHR_PATTERN.match(variant.CHROM)
chrom = chrom_match.group(2)
svtype = variant.INFO.get('SVTYPE')
if svtype:
svtype = svtype.lower()
mate_id = variant.INFO.get('MATEID')
svlen = variant.INFO.get('SVLEN')
svend = variant.INFO.get('END')
snvend = int(variant.end)
position = int(variant.POS)
ref_len = len(ref)
alt_len = len(alt)
sub_category = get_sub_category(alt_len, ref_len, category, svtype)
end = get_end(position, alt, category, snvend, svend)
length = get_length(alt_len, ref_len, category, position, end, svtype,
svlen)
end_chrom = chrom
if sub_category == 'bnd':
if ':' in alt:
match = BND_ALT_PATTERN.match(alt)
# BND will often be translocations between different chromosomes
if match:
other_chrom = match.group(1)
match = CHR_PATTERN.match(other_chrom)
end_chrom = match.group(2)
cytoband_start = get_cytoband_coordinates(chrom, position)
cytoband_end = get_cytoband_coordinates(end_chrom, end)
coordinates = {
'position': position,
'end': end,
'length': length,
'sub_category': sub_category,
'mate_id': mate_id,
'cytoband_start': cytoband_start,
'cytoband_end': cytoband_end,
'end_chrom': end_chrom,
}
return coordinates
def parse_coordinates(variant, category):
"""Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>,
'sub_category':<str>,
'mate_id':<str>,
'cytoband_start':<str>,
'cytoband_end':<str>,
}
"""
ref = variant.REF
if variant.ALT:
alt = variant.ALT[0]
if category == "str" and not variant.ALT:
alt = "."
chrom_match = CHR_PATTERN.match(variant.CHROM)
chrom = chrom_match.group(2)
svtype = variant.INFO.get("SVTYPE")
if svtype:
svtype = svtype.lower()
mate_id = variant.INFO.get("MATEID")
svlen = variant.INFO.get("SVLEN")
svend = variant.INFO.get("END")
snvend = int(variant.end)
position = int(variant.POS)
ref_len = len(ref)
alt_len = len(alt)
sub_category = get_sub_category(alt_len, ref_len, category, svtype)
end = get_end(position, alt, category, snvend, svend)
length = get_length(alt_len, ref_len, category, position, end, svtype,
svlen)
end_chrom = chrom
if sub_category == "bnd":
if ":" in alt:
match = BND_ALT_PATTERN.match(alt)
# BND will often be translocations between different chromosomes
if match:
other_chrom = match.group(1)
match = CHR_PATTERN.match(other_chrom)
end_chrom = match.group(2)
cytoband_start = get_cytoband_coordinates(chrom, position)
cytoband_end = get_cytoband_coordinates(end_chrom, end)
coordinates = {
"position": position,
"end": end,
"length": length,
"sub_category": sub_category,
"mate_id": mate_id,
"cytoband_start": cytoband_start,
"cytoband_end": cytoband_end,
"end_chrom": end_chrom,
}
return coordinates
def parse_coordinates(variant, category):
"""Find out the coordinates for a variant
Args:
variant(cyvcf2.Variant)
Returns:
coordinates(dict): A dictionary on the form:
{
'position':<int>,
'end':<int>,
'end_chrom':<str>,
'length':<int>,
'sub_category':<str>,
'mate_id':<str>,
'cytoband_start':<str>,
'cytoband_end':<str>,
}
"""
ref = variant.REF
if variant.ALT:
alt = variant.ALT[0]
if category=="str" and not variant.ALT:
alt = '.'
chrom_match = CHR_PATTERN.match(variant.CHROM)
chrom = chrom_match.group(2)
svtype = variant.INFO.get('SVTYPE')
if svtype:
svtype = svtype.lower()
mate_id = variant.INFO.get('MATEID')
svlen = variant.INFO.get('SVLEN')
svend = variant.INFO.get('END')
snvend = int(variant.end)
position = int(variant.POS)
ref_len = len(ref)
alt_len = len(alt)
sub_category = get_sub_category(alt_len, ref_len, category, svtype)
end = get_end(position, alt, category, snvend, svend)
length = get_length(alt_len, ref_len, category, position, end, svtype, svlen)
end_chrom = chrom
if sub_category == 'bnd':
if ':' in alt:
match = BND_ALT_PATTERN.match(alt)
# BND will often be translocations between different chromosomes
if match:
other_chrom = match.group(1)
match = CHR_PATTERN.match(other_chrom)
end_chrom = match.group(2)
cytoband_start = get_cytoband_coordinates(chrom, position)
cytoband_end = get_cytoband_coordinates(end_chrom, end)
coordinates = {
'position': position,
'end': end,
'length': length,
'sub_category': sub_category,
'mate_id': mate_id,
'cytoband_start': cytoband_start,
'cytoband_end': cytoband_end,
'end_chrom': end_chrom,
}
return coordinates