Created
February 3, 2023 12:07
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rotate circular sequence
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# Now, for an example with features, we’ll use a GenBank file. | |
# Suppose you have a circular genome: | |
from pydna.genbank import genbank | |
record = genbank("NC_005816.1") | |
print(record.seq[:30]) | |
# TGTAACGAACGGTGCAATAGTGATCCACAC | |
assert len(record) == 9609 | |
assert record.circular | |
assert record.description == 'Yersinia pestis biovar Microtus str. 91001 plasmid pPCP1, complete sequence' | |
assert record.dbxrefs==['BioProject:PRJNA224116', 'BioSample:SAMN02602970', 'Assembly:GCF_000007885.1'] | |
assert len(record.features) == 19 | |
shifted_record = record.shifted(2000) | |
assert len(shifted_record.features) == 19 | |
print(shifted_record.seq[:30]) | |
# GATACGCAGTCATATTTTTTACACAATTCT | |
assert sorted(ft.extract(record).seq for ft in record.features) == sorted(ft.extract(shifted_record).seq for ft in shifted_record.features) |
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