dasi.models.AlignmentGroup

class dasi.models.AlignmentGroup(alignments, group_type, name=None, meta=None)

Bases: dasi.models.alignment.AlignmentGroupBase

A representative Alignment representing a group of alignments sharing the same starting and ending position for a query sequence.

Parameters

• alignments (List[Alignment]) –

• group_type (str) –

• name (Optional[str]) –

• query_region –

• meta (Optional[dict]) –

Methods

prioritize_alignments(indices)	Prioritize alignments by pushing groupings at the given indices into the front of the alignments list.
reindex_alignments(indices)	Reindex the alignments list by index.
size_ok()	Determine if the size of this molecule is ‘acceptable’ from the bounded molecule type.
sub_region(qstart, qend, atype)	Produce a new alignment group with sub-regions of the query region and subject regions at the specified new indicies.

Attributes

query_key	Return the query key associated with the query region.
subject_keys	Return the list of subject keys in this alignment group.
subject_regions	Return the list of subject regions in this alignment group.

__init__(alignments, group_type, name=None, meta=None)

Parameters

• alignments (List[Alignment]) –

• group_type (str) –

• name (Optional[str]) –

• query_region –

• meta (Optional[dict]) –

Methods

__init__(alignments, group_type[, name, meta])	type alignments List[Alignment]
size_ok()	Determine if the size of this molecule is ‘acceptable’ from the bounded molecule type.
sub_region(qstart, qend, atype)	Produce a new alignment group with sub-regions of the query region and subject regions at the specified new indicies.

Attributes

alignments
meta
name
query_key	Return the query key associated with the query region.
query_region
subject_keys	Return the list of subject keys in this alignment group.
subject_regions	Return the list of subject regions in this alignment group.
type

prioritize_alignments(indices)

Prioritize alignments by pushing groupings at the given indices into the front of the alignments list.

Parameters

indices (List[int]) – list of indices to prioritize

Returns

None

property query_key

Return the query key associated with the query region.

Return type

str

reindex_alignments(indices)

Reindex the alignments list by index.

Parameters

indices (List[int]) – list of indices

Returns

None

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)

Produce a new alignment group with sub-regions of the query region and subject regions at the specified new indicies.

Return type

AlignmentGroupBase

property subject_keys

Return the list of subject keys in this alignment group.

Return type

List[str]

property subject_regions

Return the list of subject regions in this alignment group.

Return type

List[Region]