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
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Returns the query sequence aligned by the cigar |
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Returns the target sequence aligned by the cigar |
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Cigar formatted string for the optimal alignment |
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Optimal alignment score |
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Returns the character index at which the query sequence begins |
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Character index at where query sequence ends |
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Query sequence |
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Suboptimal alignment score |
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Character index where the target’s alignment begins |
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Character index where the target’s optimal alignment ends |
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Character index where the target’s suboptimal alignment ends |
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Target sequence |
Built-ins
Return hash(self). |
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Methods
Returns True if alignment inidices start at 0 else False |
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Set the aligment indices to start at 0 if True else 1 if False |