Identifier Containers#

An identifier container is an object which hashes identifiers.

e.g. it associates a read’s identifier to an index.

So \(\forall r \in \mathcal{R}\) we define:

\(r_{rid}\) the read’s identifier

\(r_{ind}\) the read’s index

You can write your own identifier container class using the abstract base class.

Class	Description
`AbstractIDContainer`	Abstract base class for new identifier container
`IndexIDContainer`	For 0-based indices identifiers
`HashableIDContainer`	For hashable identifiers

Type#

IdT#

Value:: Hashable

Identifier type.

Indices Identifier Container#

class IndexIDContainer#

Reads identifier container for 0-based indentifiers.

Methods:

`__contains__`(read_id)	Return True if read's identifier in container.
`__iter__`()	Iterate on reads' identifier.
`__len__`()	Return the number of recorded read's identifiers.
`add`(read_id)	Add an entry if identifier not yet recorded.
`id_to_indor`(read_id[, orientation])	Return the oriented vertex associated to the id.
`indor_to_id`(vertex)	Return the id from vertices.
`pop`(read_id)	Remove read's identifier.

__contains__(read_id)#

Return True if read’s identifier in container.

Parameters:: read_id (IndexT) – Read’s identifier
Returns:: Is read’s identifier in container?
Return type:: bool

__iter__()#

Iterate on reads’ identifier.

Yields:: IndexT – Reads’ identifier

__len__()#

Return the number of recorded read’s identifiers.

Returns:: Number of reads’ identifiers
Return type:: int

add(read_id)#

Add an entry if identifier not yet recorded.

Parameters:: read_id (IndexT) – Read’s identifier
Returns:: Associated vertex index
Return type:: IndexT

Notes

It considers bijective-property respected (read’s identifiers are 0-base indices), thus it adds all read’s identifiers between the \(max(r_{id} \in \mathcal{R_{id}}\) and new \(r_{id}\)

If the property was violated, only new \(r_{id}\) is added.

id_to_indor(read_id, orientation=FORWARD_INT)#

Return the oriented vertex associated to the id.

Parameters:

read_id (IdT) – Read’s identifier
orientation (OrT, default FORWARD_INT) – Read orientation

Returns:

Oriented vertex

Return type:

IndOrT

Raises:

NoReadId – If there is no read’s identifier in container

indor_to_id(vertex)#

Return the id from vertices.

Parameters:: vertex (IndOrT) – Oriented vertex
Returns:: The associated read’s identifier
Return type:: IndexT
Raises:: NoVertexIndex – There is no read’s identifier corresponding to given vertex

pop(read_id)#

Remove read’s identifier.

Parameters:: read_id (int) – Read’s identifier
Returns:: Index corresponding to read’s identifier
Return type:: IndexT
Raises:: NoReadId – If there is no read’s identifier in container

Hashable Identifier Container#

class HashableIDContainer#

Reads identifier container for hashable identifiers.

Methods:

`__contains__`(read_id)	Return True if read's identifier in container.
`__iter__`()	Iterate on reads' identifier.
`__len__`()	Return the number of recorded read's identifiers.
`add`(read_id)	Add an entry if identifier not yet recorded else corresponding index.
`id_to_indor`(read_id[, orientation])	Return the oriented vertex associated to the id.
`indor_to_id`(vertex)	Return the id from vertices.
`pop`(read_id)	Remove read's identifier.

__contains__(read_id)#

Return True if read’s identifier in container.

Parameters:: read_id (Hashable) – Read’s identifier
Returns:: Is read’s identifier in container?
Return type:: bool

__iter__()#

Iterate on reads’ identifier.

Yields:: Hashable – Reads’ identifier

__len__()#

Return the number of recorded read’s identifiers.

Returns:: Number of reads’ identifiers
Return type:: int

add(read_id)#

Add an entry if identifier not yet recorded else corresponding index.

Parameters:: read_id (Hasable) – Read’s identifier
Returns:: Associated vertex index
Return type:: IndexT

id_to_indor(read_id, orientation=FORWARD_INT)#

Return the oriented vertex associated to the id.

Parameters:

read_id (Hashable) – Read’s identifier
orientation (OrT, default FORWARD_INT) – Read orientation

Returns:

Oriented vertex

Return type:

IndOrT

Raises:

NoReadId – If there is no read’s identifier in container

indor_to_id(vertex)#

Return the id from vertices.

Parameters:: vertex (IndOrT) – Oriented vertex
Returns:: The associated read’s identifier
Return type:: Hashable
Raises:: NoVertexIndex – There is no read’s identifier corresponding to given vertex

pop(read_id)#

Remove read’s identifier.

Parameters:: read_id (Hashable) – Read’s identifier
Returns:: Index corresponding to read’s identifier
Return type:: IndexT
Raises:: NoReadId – If there is no read’s identifier in container

Identifier Container Abstract Base Class#

class AbstractIDContainer#

Abstract class for reads identifiers container.

Methods:

`__contains__`(read_id)	Return True if read's identifier in container.
`__iter__`()	Iterate on reads' identifier.
`__len__`()	Return the number of recorded read's identifiers.
`add`(read_id)	Add an entry if identifier not yet recorded else corresponding index.
`id_to_indor`(read_id[, orientation])	Return the oriented vertex associated to the id.
`indor_to_id`(vertex)	Return the id from vertices.
`pop`(read_id)	Remove read's identifier.

abstract __contains__(read_id)#

Return True if read’s identifier in container.

Parameters:: read_id (IdT) – Read’s identifier
Returns:: Is read’s identifier in container?
Return type:: bool

abstract __iter__()#

Iterate on reads’ identifier.

Yields:: IdT – Reads’ identifier

abstract __len__()#

Return the number of recorded read’s identifiers.

Returns:: Number of reads’ identifiers
Return type:: int

abstract add(read_id)#

Add an entry if identifier not yet recorded else corresponding index.

Parameters:: read_id (IdT) – Read’s identifier
Returns:: Associated vertex index
Return type:: IndexT

abstract id_to_indor(read_id, orientation=FORWARD_INT)#

Return the oriented vertex associated to the id.

Parameters:

read_id (IdT) – Read’s identifier
orientation (OrT, default FORWARD_INT) – Read orientation

Returns:

Oriented vertex

Return type:

IndOrT

Raises:

NoReadId – If there is no read’s identifier in container

abstract indor_to_id(vertex)#

Return the id from vertices.

Parameters:: vertex (IndOrT) – Oriented vertex
Returns:: The associated read’s identifier
Return type:: IdT
Raises:: NoVertex – There is no read’s identifier corresponding to given vertex

abstract pop(read_id)#

Remove read’s identifier.

Parameters:: read_id (IdT) – Read’s identifier
Returns:: Index corresponding to read’s identifier
Return type:: IndexT
Raises:: NoReadId – If there is no read’s identifier in container