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

Methods

is_zero_based Returns True if alignment inidices start at 0 else False
set_zero_based Set the aligment indices to start at 0 if True else 1 if False