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
Returns the query sequence aligned by the cigar
Returns the target sequence aligned by the cigar
Cigar formatted string for the optimal alignment
Optimal alignment score
Returns the character index at which the query sequence begins
Character index at where query sequence ends
Query sequence
Suboptimal alignment score
Character index where the target's alignment begins
Character index where the target's optimal alignment ends
Character index where the target's suboptimal alignment ends
Target sequence
Methods
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
Special methods
__getitem__(key, /)Return self[key].
__str__(/)Return str(self).
Special methods (inherited)
__eq__(value, /)Return self==value.
__ge__(value, /)Return self>=value.
__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.
Details
- aligned_query_sequence#
Returns the query sequence aligned by the cigar
- Returns:
- str
Aligned query sequence
Notes
This will return None if suppress_sequences was True when this object was created
- aligned_target_sequence#
Returns the target sequence aligned by the cigar
- Returns:
- str
Aligned target sequence
Notes
This will return None if suppress_sequences was True when this object was created
- cigar#
Cigar formatted string for the optimal alignment
- Returns:
- str
The cigar string of the optimal alignment
Notes
The cigar string format is described in [1] and [2].
If there is no cigar or optimal alignment, this will return an empty string
References
- optimal_alignment_score#
Optimal alignment score
- Returns:
- int
The optimal alignment score
- query_begin#
Returns the character index at which the query sequence begins
- Returns:
- int
The character index of the query sequence beginning
Notes
The result is a 0-based index by default
- query_end#
Character index at where query sequence ends
- Returns:
- int
The character index of the query sequence ending
Notes
The result is a 0-based index by default
- query_sequence#
Query sequence
- Returns:
- str
The query sequence
- suboptimal_alignment_score#
Suboptimal alignment score
- Returns:
- int
The suboptimal alignment score
- target_begin#
Character index where the target’s alignment begins
- Returns:
- int
The character index of the target sequence’s alignment’s beginning
Notes
The result is a 0-based index by default
- target_end_optimal#
Character index where the target’s optimal alignment ends
- Returns:
- int
- The character index of the target sequence’s optimal alignment’s
end
Notes
The result is a 0-based index by default
- target_end_suboptimal#
Character index where the target’s suboptimal alignment ends
- Returns:
- int
- The character index of the target sequence’s suboptimal alignment’s
end
Notes
The result is a 0-based index by default
- target_sequence#
Target sequence
- Returns:
- str
The target sequence
- __getitem__(key, /)#
Return self[key].
- __setstate__()#
- __str__(/)#
Return str(self).