SequencePairProperties.py - Computing metrics for aligned sequences¶
This module provides methods for extracting and reporting sequence
properties of aligned nucleotide sequences such as percent identity,
substitution rate, etc. Usage is the same as
SequencePairProperties
.
Reference¶
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class
SequencePairProperties.
SequencePairPropertiesDistance
(*args, **kwargs)¶ Bases:
SequencePairProperties.SequencePairProperties
base class for distance estimators.
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class
SequencePairProperties.
SequencePairPropertiesBaseML
(options, *args, **kwargs)¶ Bases:
SequencePairProperties.SequencePairPropertiesDistance
Counts for nucleic acid sequences.
The first characters are ACGT.
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loadPair
(seq1, seq2)¶ load sequence properties from a pair.
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class
SequencePairProperties.
SequencePairPropertiesCountsNa
(*args, **kwargs)¶ Bases:
SequencePairProperties.SequencePairProperties
Counts for nucleic acid sequences.
The first characters are ACGT.
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buildSubstitutionMatrix
(seq1, seq2, alphabet)¶ given a pair of sequences, calculate a substitution matrix for the given alphabet.
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loadPair
(seq1, seq2)¶ load sequence properties from a pair.
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class
SequencePairProperties.
SequencePairPropertiesCountsCodons
¶ Bases:
SequencePairProperties.SequencePairPropertiesCountsNa
the first characters are ACGT.
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class
SequencePairProperties.
SequencePairPropertiesPID
(*args, **kwargs)¶ Bases:
SequencePairProperties.SequencePairPropertiesDistance
Percent identity.
The percent identity is the ratio of the number of identical residues divided by the number of aligned residues.
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loadPair
(seq1, seq2)¶ load sequence properties from a pair.
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