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

Special methods

__getitem__(key, /)	Return self[key].
__setstate__
__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

[1]

http://genome.sph.umich.edu/wiki/SAM

[2]

http://samtools.github.io/hts-specs/SAMv1.pdf

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).