biocantor.sequence.sequence

Module Contents

Classes

Sequence

Attributes

Location

Sequence

ParentInputType

biocantor.sequence.sequence.Location
biocantor.sequence.sequence.Sequence
biocantor.sequence.sequence.ParentInputType
class biocantor.sequence.sequence.Sequence(data: str, alphabet: inscripta.biocantor.sequence.alphabet.Alphabet, id: Optional[str] = None, type: Optional[Union[inscripta.biocantor.parent.SequenceType, str]] = None, parent: Optional[ParentInputType] = None, validate_alphabet: bool = True, validate_parent: bool = True)

Bases: inscripta.biocantor.AbstractSequence

A sequence with an alphabet

property parent_id: Optional[str]
property is_empty: bool

Is this a len 0 sequence?

property location_on_parent: Optional[Location]

Location of this sequence relative to the parent

property parent_strand: Optional[inscripta.biocantor.location.strand.Strand]

Strand of this sequence

property parent_type: Optional[str]
__slots__ = []
__eq__(other)

Return self==value.

__hash__()

Return hash(self).

__str__()

Returns the sequence data as a string

__getitem__(key: Union[int, slice]) → Sequence

Returns a slice of the current Sequence as a new Sequence object

__repr__()

Return repr(self).

summary() → str

Returns a short string summary of this Sequence

_validate_alphabet()

Raises AlphabetError if this Sequence does not conform to its alphabet

static validate_alphabet(sequence, alphabet)
reverse_complement(new_id: str = None, new_type: str = None) → Sequence

Returns a new Sequence corresponding to the reverse complement of this Sequence. Location on parent, if it exists, is converted appropriately.

Parameters

  • new_id – ID for the returned Sequence. If no value is provided, None is used.

  • new_type – Sequence type for the returned Sequence. If no value is provided, None is used.

append(other: Sequence, new_id: Optional[str] = None, data_only: bool = False) → Sequence

Returns a new Sequence consisting of other sequence appended to the end of this Sequence

Parameters

  • other – Other sequence

  • new_id – ID for the returned sequence

  • data_only – Only combine sequence data, ignoring and removing metadata such as sequence type and parent info. If False, all metadata for both sequences must be consistent, and the returned sequence will have appropriate combined metadata.

first_ancestor_of_type(sequence_type: str, include_self: bool = True) → inscripta.biocantor.parent.Parent

Returns the Parent object representing the closest ancestor (parent, parent of parent, etc.) of this sequence which has the given sequence type. If include_self is True and this sequence has the given type, returns a new Parent object representing this sequence. Raises NoSuchAncestorException if no ancestor with the given type exists.

Parameters

  • sequence_type – Sequence type

  • include_self – Include this sequence as a candidate

has_ancestor_of_type(sequence_type: str, include_self: bool = True) → bool

Returns True if some ancestor (parent, parent of parent, etc.) of this sequence which has the given sequence type, or False otherwise. If include_self is True and this sequence has the given type, returns True.

Parameters

  • sequence_type – Sequence type

  • include_self – Include this sequence as a candidate

to_fasta(num_chars: Optional[int] = 60) → str

Returns a FASTA-formatted string for this sequence. These are line-broken every num_chars.

Parameters

num_chars – Number of characters per line. Defaults to 60, which is the same as BioPython.