dasi.models.AlignmentContainer¶

class dasi.models.AlignmentContainer(seqdb, alignments=None)[source]¶

Bases: collections.abc.Sized

Container for a set of query-to-subject alignments for a single query.

Instance Attributes/Properties:

alignments list of alignments for the container: List[Alignment]
seqdb key to SeqRecord dictionary: Dict[str, SeqRecord]
logger the instance’s logger: Loggable

This class contains:

Methods grouping alignments together according to those

alignments that share the same starting and ending points.

Methods for ‘expanding’ alignments

Methods

`_alignment_hash`(a)	A hashable representation of an alignment for grouping.
`_create_pcr_product_alignment`(…)	Create a new alignment group for a PCR product.
`_make_subgroup`(group, a, b, atype)	Make a subgroup at the specified indices.
`clean_alignments`()	Remove redundant alignments.
`copy_groups`(alignment_groups, atype)	Copy alignments from the list of groups to a new alignment type.
`expand`([expand_overlaps, expand_primers, …])	Alignment expansion algorithm.
`expand_overlaps`(alignment_groups[, atype, …])	Expand the list of alignments from existing regions.
`expand_primer_pairs`(alignment_groups[, lim_size])	Creates new alignments for all possible primer pairs.
`find_groups_by_pos`(a, b, group_type[, groups])	Return a list of groups that have the same positions (a, b) and same group_type.
`freeze`()	Freeze the container, disallowing further modifications to alignments.
`get_groups_by_types`(types)	Return AlignmentGroups by fragment type.
`groups_by_type`()	Return alignment groups according to their alignment ‘type’.
`redundent_alignment_groups`(alignments)	Return AlignmentGroups that have been grouped by alignment_hash.
`unfreeze`()	Unfreeze the container, allowing modifications to alignments.

Attributes

types

Return all valid types.

__init__(seqdb, alignments=None)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(seqdb[, alignments])	Initialize self.
`expand`([expand_overlaps, expand_primers, …])	Alignment expansion algorithm.
`expand_overlaps`(alignment_groups[, atype, …])	Expand the list of alignments from existing regions.
`expand_primer_extension_products`([…])
`expand_primer_pairs`(alignment_groups[, lim_size])	Creates new alignments for all possible primer pairs.
`filter_alignments_by_span`(alignments, region)
`find_groups_by_pos`(a, b, group_type[, groups])	Return a list of groups that have the same positions (a, b) and same group_type.
`freeze`()	Freeze the container, disallowing further modifications to alignments.
`get_alignments_by_types`(types)	rtype `List`[`Alignment`]
`get_groups_by_types`(types)	Return AlignmentGroups by fragment type.
`groups`()	rtype `List`[`Union`[`AlignmentGroup`, `MultiPCRProductAlignmentGroup`]]
`groups_by_type`()	Return alignment groups according to their alignment ‘type’.
`pcr_alignment_groups`()
`redundent_alignment_groups`(alignments)	Return AlignmentGroups that have been grouped by alignment_hash.
`unfreeze`()	Unfreeze the container, allowing modifications to alignments.

Attributes

`alignments`
`types`	Return all valid types.
`valid_types`

static _alignment_hash(a)[source]¶: A hashable representation of an alignment for grouping.

_create_pcr_product_alignment(template_group, fwd, rev, alignment_type, lim_size)[source]¶

Create a new alignment group for a PCR product.

Situations the PCRProductAlignmentGroup represents:

            <--------
------------------
---->

               <--------
   ------------------
-------->


        <-----
   ------------------
-------->


              <------
   ------------------
-------->

Parameters

template_group (AlignmentGroup) –
fwd (Optional[Alignment]) –
rev (Optional[Alignment]) –
alignment_type (str) –

Returns

_make_subgroup(group, a, b, atype)[source]¶

Make a subgroup at the specified indices.

Returns None if a, b and the indices of the group.query_region or if a == b

Return type: Optional[AlignmentGroup]

clean_alignments()[source]¶: Remove redundant alignments.

copy_groups(alignment_groups, atype)[source]¶: Copy alignments from the list of groups to a new alignment type.

expand(expand_overlaps=True, expand_primers=True, expand_primer_dimers=False, lim_size=True)[source]¶

Alignment expansion algorithm.

Parameters

expand_overlaps – if True, expand overlaps
expand_primers – if True, expand primer pairs
expand_primer_dimers – if True, expand primer dimer pairs
lim_size (bool) – if True, limit the size of the alignment according to theri Molecule definitions

Returns

None

expand_overlaps(alignment_groups, atype='PCR_PRODUCT', lim_size=True, pass_condition=None, include_left=True)[source]¶

Expand the list of alignments from existing regions. Produces new fragments in the following two situations:

if `include_left`
|--------|          alignment 1
    |--------|      alignment 2
|---|               new alignment


|--------|          alignment 1
     |--------|     alignment 2
     |---|          new alignment

Parameters

alignment_groups (List[AlignmentGroup]) – list of alignment groups to expand
atype – the alignment type label for expanded alignments
lim_size (bool) – if True, only add alignments that pass the size limitations
pass_condition (Optional[Callable]) – an optional callable that takes group_a (AlignmentGroup) and group_b (AlignmentGroup). If the returned value is False, alignments are skipped.
include_left (bool) – if True, will add overlapping region and the left region up to the overlap.

Return type

List[Alignment]

Returns

list of new alignments

expand_primer_pairs(alignment_groups, lim_size=True)[source]¶

Creates new alignments for all possible primer pairs. Searches for fwd and rev primer pairs that exist within other alignments and produces all combinations of alignments that can form from these primer pairs.

Return type: List[Alignment]
Returns: list

find_groups_by_pos(a, b, group_type, groups=None)[source]¶

Return a list of groups that have the same positions (a, b) and same group_type.

Parameters

a (int) – starting position
b (int) – ending position
group_type (str) – group_type
groups – optional list of groups to search

Return type

List[Union[AlignmentGroup, PCRProductAlignmentGroup]]

Returns

list of groups

freeze()[source]¶: Freeze the container, disallowing further modifications to alignments.

get_groups_by_types(types)[source]¶

Return AlignmentGroups by fragment type.

Parameters: types (List[str]) – list of types
Return type: Union[AlignmentGroup, List[AlignmentGroup]]
Returns

groups_by_type()[source]¶

Return alignment groups according to their alignment ‘type’.

Return type: Dict[str, List[Union[AlignmentGroup, PCRProductAlignmentGroup]]]
Returns: dict

classmethod redundent_alignment_groups(alignments)[source]¶

Return AlignmentGroups that have been grouped by alignment_hash.

Parameters: alignments (List[Alignment]) –
Return type: List[AlignmentGroup]
Returns

property types¶

Return all valid types.

Return type: Tuple[Any, …]
Returns

unfreeze()[source]¶: Unfreeze the container, allowing modifications to alignments.