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
__init_subclass__ |
This method is called when a class is subclassed. |
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 |