dasi.models.Alignment

class dasi.models.Alignment(query_region, subject_region, atype, query_key, subject_key, meta=None)

Bases: dasi.models.alignment.RepresentsMolecule, collections.abc.Sized

A pair of Regions that ‘aligns’ two regions of DNA sequences. All regions must always be the same length.

A subregion of both regions may be taken.

Makes an alignment between two regions of sequences. Validates the regions are the same length.

Parameters

• query_region (Region) – Query region this alignment aligns to

• subject_region (Region) – Subject region this alignment aligns to.

• atype (str) – Type of alignment

• query_key (str) – The record identifier for the query

• subject_key (str) – The record identifier for the subject

Methods

copy([atype])	Do shallow copy of this alignment.
size_ok()	Determine if the size of this molecule is ‘acceptable’ from the bounded molecule type.
sub_region(qstart, qend[, atype])	Returns a copy of the alignment between the inclusive start and end relative to the query region.

__init__(query_region, subject_region, atype, query_key, subject_key, meta=None)

Makes an alignment between two regions of sequences. Validates the regions are the same length.

Parameters

• query_region (Region) – Query region this alignment aligns to

• subject_region (Region) – Subject region this alignment aligns to.

• atype (str) – Type of alignment

• query_key (str) – The record identifier for the query

• subject_key (str) – The record identifier for the subject

Methods

__init__(query_region, subject_region, …)	Makes an alignment between two regions of sequences.
copy([atype])	Do shallow copy of this alignment.
eq_hash()
is_perfect_subject()
size_ok()	Determine if the size of this molecule is ‘acceptable’ from the bounded molecule type.
sub_region(qstart, qend[, atype])	Returns a copy of the alignment between the inclusive start and end relative to the query region.
validate()

Attributes

query_key
query_region
subject_key
subject_region
type
uid

copy(atype=None)

Do shallow copy of this alignment. Query and subject regions between this and the copied alignment will be identical.

Parameters

atype – new alignment type

Return type

Alignment

Returns

size_ok()

Determine if the size of this molecule is ‘acceptable’ from the bounded molecule type.

Returns

whether this passes the size requirement of the molecule type.

sub_region(qstart, qend, atype=None)

Returns a copy of the alignment between the inclusive start and end relative to the query region.

Parameters

• qstart (int) – start of the query sub region

• qend (int) – end of the query sub region

• atype – optional type of alignment to return

Return type

Alignment

Returns