skbio.alignment.AlignmentStructure#

class skbio.alignment.AlignmentStructure#

Wraps the result of an alignment c struct so it is accessible to Python

Notes

cigar may be empty depending on parameters used.

target_begin and query_begin may be -1 depending on parameters used.

Developer note: read_sequence is an alias for query_sequence used by ssw.c as is reference_sequence for target_sequence

Attributes

aligned_query_sequence

Returns the query sequence aligned by the cigar

aligned_target_sequence

Returns the target sequence aligned by the cigar

cigar

Cigar formatted string for the optimal alignment

optimal_alignment_score

Optimal alignment score

query_begin

Returns the character index at which the query sequence begins

query_end

Character index at where query sequence ends

query_sequence

Query sequence

suboptimal_alignment_score

Suboptimal alignment score

target_begin

Character index where the target's alignment begins

target_end_optimal

Character index where the target's optimal alignment ends

target_end_suboptimal

Character index where the target's suboptimal alignment ends

target_sequence

Target sequence

Built-ins

__eq__(value, /)

Return self==value.

__ge__(value, /)

Return self>=value.

__getitem__(key, /)

Return self[key].

__getstate__(/)

Helper for pickle.

__gt__(value, /)

Return self>value.

__hash__(/)

Return hash(self).

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.

__setstate__

__str__(/)

Return str(self).

Methods

is_zero_based()

Returns True if alignment inidices start at 0 else False

set_zero_based(is_zero_based)

Set the aligment indices to start at 0 if True else 1 if False