def __call__(self, read1: DnaSequence, read2: DnaSequence,
info1: ModificationInfo,
info2: ModificationInfo) -> Tuple[DnaSequence, DnaSequence]:
id1, comment1 = Renamer.parse_name(read1.name)
id2, comment2 = Renamer.parse_name(read2.name)
if not record_names_match(read1.name, read2.name):
raise ValueError(
"Input read IDs not identical: '{}' != '{}'".format(id1, id2))
name1, name2 = self.get_new_headers(
id1=id1,
id2=id2,
comment1=comment1,
comment2=comment2,
header1=read1.name,
header2=read2.name,
info1=info1,
info2=info2,
)
new_id1 = Renamer.parse_name(name1)[0]
new_id2 = Renamer.parse_name(name2)[0]
if not record_names_match(name1, name2):
raise InvalidTemplate(
"After renaming R1 and R2, their IDs are no longer identical: "
"'{}' != '{}'. Original read ID: '{}'. ".format(
new_id1, new_id2, id1))
read1.name = name1
read2.name = name2
return read1, read2
def __call__(self, read: DnaSequence, info: ModificationInfo) -> DnaSequence:
id_, comment = self.parse_name(read.name)
read.name = self._template.format(
header=read.name,
id=id_,
comment=comment,
cut_prefix=info.cut_prefix if info.cut_prefix else "",
cut_suffix=info.cut_suffix if info.cut_suffix else "",
adapter_name=info.matches[-1].adapter.name if info.matches else "no_adapter",
rc="rc" if info.is_rc else "",
)
return read
