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

class SequencePairProperties.SequencePairPropertiesDistance(*args, **kwargs)

Bases: SequencePairProperties.SequencePairProperties

base class for distance estimators.

class SequencePairProperties.SequencePairPropertiesBaseML(options, *args, **kwargs)

Bases: SequencePairProperties.SequencePairPropertiesDistance

Counts for nucleic acid sequences.

The first characters are ACGT.

loadPair(seq1, seq2)

load sequence properties from a pair.

class SequencePairProperties.SequencePairPropertiesCountsNa(*args, **kwargs)

Bases: SequencePairProperties.SequencePairProperties

Counts for nucleic acid sequences.

The first characters are ACGT.

buildSubstitutionMatrix(seq1, seq2, alphabet)

given a pair of sequences, calculate a substitution matrix for the given alphabet.

loadPair(seq1, seq2)

load sequence properties from a pair.

class SequencePairProperties.SequencePairPropertiesCountsCodons

Bases: SequencePairProperties.SequencePairPropertiesCountsNa

the first characters are ACGT.

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.

loadPair(seq1, seq2)

load sequence properties from a pair.