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mavis/annotate/genomic

class Template

inherits BioInterval

class IntergenicRegion

inherits BioInterval

IntergenicRegion.key()

see :func:structural_variant.annotate.base.BioInterval.key

def key(self):

IntergenicRegion.chr()

returns the name of the chromosome that this region resides on

@property
def chr(self):

Args

  • self

IntergenicRegion.to_dict()

see :func:structural_variant.annotate.base.BioInterval.to_dict

def to_dict(self):

class Gene

inherits BioInterval

Gene.transcript_priority()

prioritizes transcripts from 0 to n-1 based on best transcript flag and then alphanumeric name sort

def transcript_priority(self, transcript):

Args

  • transcript

Warning

Lower number means higher priority. This is to make sort work by default

Gene.transcripts()

list of unspliced transcripts

@property
def transcripts(self) -> List['PreTranscript']:

Args

  • self

Returns

Gene.translations()

list of translations

@property
def translations(self) -> List[Translation]:

Args

  • self

Returns

Gene.chr()

returns the name of the chromosome that this gene resides on

@property
def chr(self):

Args

  • self

Gene.key()

see :func:structural_variant.annotate.base.BioInterval.key

def key(self):

Gene.get_seq()

gene sequence is always given wrt to the positive forward strand regardless of gene strand

def get_seq(self, reference_genome: ReferenceGenome, ignore_cache: bool = False) -> str:

Args

  • reference_genome (ReferenceGenome): dict of reference sequence by template/chr name
  • ignore_cache (bool): if True then stored sequences will be ignored and the function will attempt to retrieve the sequence using the positions and the input reference_genome

Returns

  • str: the sequence of the gene

Gene.spliced_transcripts()

list of transcripts

@property
def spliced_transcripts(self) -> List['Transcript']:

Args

  • self

Returns

Gene.to_dict()

see :func:structural_variant.annotate.base.BioInterval.to_dict

def to_dict(self):

class Exon

inherits BioInterval

Exon.transcript()

PreTranscript: the transcript this exon belongs to

@property
def transcript(self):

Args

  • self

Exon.donor_splice_site()

the genomic range describing the splice site

@property
def donor_splice_site(self) -> SpliceSite:

Args

  • self

Returns

Exon.acceptor_splice_site()

the genomic range describing the splice site

@property
def acceptor_splice_site(self) -> SpliceSite:

Args

  • self

Returns

Exon.donor()

returns the genomic exonic position of the donor splice site

@property
def donor(self) -> int:

Args

  • self

Returns

  • int

Exon.acceptor()

returns the genomic exonic position of the acceptor splice site

@property
def acceptor(self) -> int:

Args

  • self

Returns

  • int

class PreTranscript

inherits BioInterval

PreTranscript.__init__()

creates a new transcript object

def __init__(
    self,
    exons: List[Exon],
    gene: Optional[Gene] = None,
    name: Optional[str] = None,
    strand: Optional[str] = None,
    spliced_transcripts: Optional[List['Transcript']] = None,
    seq: Optional[str] = None,
    is_best_transcript: bool = False,
):

Args

  • exons (List[Exon]): list of Exon that make up the transcript
  • gene (Optional[Gene]): the gene this transcript belongs to
  • name (Optional[str]): name of the transcript
  • strand (Optional[str]): strand the transcript is on, defaults to the strand of the Gene if not specified
  • spliced_transcripts (Optional[List[Transcript]])
  • seq (Optional[str]): unspliced cDNA seq
  • is_best_transcript (bool)

PreTranscript.generate_splicing_patterns()

returns a list of splice sites to be connected as a splicing pattern

def generate_splicing_patterns(self) -> List[SplicingPattern]:

Returns

Note

see theory - predicting splicing patterns

PreTranscript.gene()

Gene: the gene this transcript belongs to

@property
def gene(self):

Args

  • self

PreTranscript.convert_genomic_to_nearest_cdna()

converts a genomic position to its cdna equivalent or (if intronic) the nearest cdna and shift

def convert_genomic_to_nearest_cdna(
    self, pos: int, splicing_pattern: SplicingPattern, stick_direction=None, allow_outside=True
) -> Tuple[int, int]:

Args

  • pos (int): the genomic position
  • splicing_pattern (SplicingPattern): the splicing pattern
  • stick_direction
  • allow_outside

Returns

  • Tuple[int, int]: the exonic cdna position and the intronic shift

PreTranscript.exon_number()

exon numbering is based on the direction of translation

def exon_number(self, exon: Exon) -> int:

Args

  • exon (Exon): the exon to be numbered

Returns

  • int: the exon number (1 based)

Raises

  • AttributeError: if the strand is not given or the exon does not belong to the transcript

PreTranscript.translations()

list of translations associated with this transcript

@property
def translations(self) -> List[Translation]:

Args

  • self

Returns

PreTranscript.transcripts()

list of spliced transcripts

@property
def transcripts(self) -> List['Transcript']:

Args

  • self

Returns

class Transcript

inherits BioInterval

Attributes

Transcript.__init__()

splicing pattern is given in genomic coordinates

def __init__(
    self,
    pre_transcript: PreTranscript,
    splicing_patt: SplicingPattern,
    seq: Optional[str] = None,
    translations: Optional[List[Translation]] = None,
):

Args

  • pre_transcript (PreTranscript): the unspliced transcript
  • splicing_patt (SplicingPattern): the list of splicing positions
  • seq (Optional[str]): the cdna sequence
  • translations (Optional[List[Translation]]): the list of translations of this transcript

Transcript.unspliced_transcript()

the unspliced transcript this splice variant belongs to

@property
def unspliced_transcript(self) -> PreTranscript:

Args

  • self

Returns