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