answer.dbxrefs = self.dbxrefs[:]
if isinstance(features, list):
answer.features = features
elif features:
# Copy the old features, adjusting location and string
l = len(answer)
answer.features = [f._flip(l) for f in self.features]
# The old list should have been sorted by start location,
# reversing it will leave it sorted by what is now the end position,
# so we need to resort in case of overlapping features.
# NOTE - In the common case of gene before CDS (and similar) with
# the exact same locations, this will still maintain gene before CDS
answer.features.sort(key=lambda x: x.location.start.position)
if isinstance(annotations, dict):
answer.annotations = annotations
elif annotations:
# Copy the old annotations,
answer.annotations = self.annotations.copy()
if isinstance(letter_annotations, dict):
answer.letter_annotations = letter_annotations
elif letter_annotations:
# Copy the old per letter annotations, reversing them
for key, value in self.letter_annotations.items():
answer._per_letter_annotations[key] = value[::-1]
return answer
if __name__ == "__main__":
from anarci.Bio._utils import run_doctest
run_doctest()
else:
id = self.clean(record.id)
description = self.clean(record.description)
if description and description.split(None, 1)[0] == id:
# The description includes the id at the start
title = description
elif description:
title = "%s %s" % (id, description)
else:
title = id
assert "\n" not in title
assert "\r" not in title
self.handle.write(">%s\n" % title)
data = self._get_seq_string(record) # Catches sequence being None
assert "\n" not in data
assert "\r" not in data
if self.wrap:
for i in range(0, len(data), self.wrap):
self.handle.write(data[i:i + self.wrap] + "\n")
else:
self.handle.write(data + "\n")
if __name__ == "__main__":
from anarci.Bio._utils import run_doctest
run_doctest(verbose=0)