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Issue 4940 - Loosen restriction of FormattedSeq._table in Restriction module #4941

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Merged
peterjc merged 3 commits into from
Feb 19, 2025
Merged

Issue 4940 - Loosen restriction of FormattedSeq._table in Restriction module #4941

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7a6743e
closes #4940
manulera Feb 18, 2025
a40aaf7
Update Restriction.py
manulera Feb 19, 2025
2527e9a
fix test
manulera Feb 19, 2025
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4 changes: 3 additions & 1 deletion Bio/Restriction/Restriction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,9 @@
def _make_FormattedSeq_table() -> bytes:
table = bytearray(256)
upper_to_lower = ord("A") - ord("a")
for c in b"ABCDGHKMNRSTVWY": # Only allow IUPAC letters
# Only allow alphabetic characters
# (although only ACGT are used for finding restriction sites)
for c in b"ABCDEFGHIJKLMNOPQRSTUVWXYZ":
table[c] = c # map uppercase to uppercase
table[c - upper_to_lower] = c # map lowercase to uppercase
return bytes(table)
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9 changes: 6 additions & 3 deletions Tests/test_Restriction.py
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Expand Up @@ -52,10 +52,13 @@ def test_sequence_object(self):
EcoRI.search(Seq("ATGC"))
EcoRI.search(MutableSeq("TCAG"))

def test_non_iupac_letters(self):
"""Test if non-IUPAC letters raise a TypeError."""
def test_non_allowed_characters(self):
"""Test if non-allowed characters raise a TypeError."""
# Any letter is accepted, even if it's not a nucleotide
FormattedSeq(Seq("ABCDEFGHIJKLMNOPQRSTUVWXYZ"))
# Other characters are not accepted
with self.assertRaises(TypeError):
seq = FormattedSeq(Seq("GATCZ"))
FormattedSeq(Seq("GATCZE-"))

def test_formatted_seq(self):
"""Test several methods of FormattedSeq."""
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