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mavis.annotate.genomic

class mavis.annotate.genomic.Template

inherits BioInterval

class mavis.annotate.genomic.IntergenicRegion

inherits BioInterval

mavis.annotate.genomic.IntergenicRegion.key()

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

def key(self):

mavis.annotate.genomic.IntergenicRegion.chr()

returns the name of the chromosome that this region resides on

@property
def chr(self):

Args

  • self

mavis.annotate.genomic.IntergenicRegion.to_dict()

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

def to_dict(self):

class mavis.annotate.genomic.Gene

inherits BioInterval

mavis.annotate.genomic.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

mavis.annotate.genomic.Gene.transcripts()

List[PreTranscript] list of unspliced transcripts

@property
def transcripts(self):

Args

  • self

mavis.annotate.genomic.Gene.translations()

List[mavis.annotate.protein.Translation] list of translations

@property
def translations(self):

Args

  • self

mavis.annotate.genomic.Gene.chr()

returns the name of the chromosome that this gene resides on

@property
def chr(self):

Args

  • self

mavis.annotate.genomic.Gene.key()

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

def key(self):

mavis.annotate.genomic.Gene.get_seq()

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

def get_seq(self, reference_genome, ignore_cache=False):

Args

  • reference_genome (Dict[str,Bio.SeqRecord]): dict of reference sequence by
  • 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

mavis.annotate.genomic.Gene.spliced_transcripts()

List[Transcript]: list of transcripts

@property
def spliced_transcripts(self):

Args

  • self

mavis.annotate.genomic.Gene.to_dict()

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

def to_dict(self):

class mavis.annotate.genomic.Exon

inherits BioInterval

mavis.annotate.genomic.Exon.transcript()

PreTranscript: the transcript this exon belongs to

@property
def transcript(self):

Args

  • self

mavis.annotate.genomic.Exon.donor_splice_site()

mavis.interval.Interval: the genomic range describing the splice site

@property
def donor_splice_site(self):

Args

  • self

mavis.annotate.genomic.Exon.acceptor_splice_site()

mavis.interval.Interval: the genomic range describing the splice site

@property
def acceptor_splice_site(self):

Args

  • self

mavis.annotate.genomic.Exon.donor()

int: returns the genomic exonic position of the donor splice site

@property
def donor(self):

Args

  • self

mavis.annotate.genomic.Exon.acceptor()

int: returns the genomic exonic position of the acceptor splice site

@property
def acceptor(self):

Args

  • self

class mavis.annotate.genomic.PreTranscript

inherits BioInterval

mavis.annotate.genomic.PreTranscript.__init__()

creates a new transcript object

def __init__(
    self,
    exons,
    gene=None,
    name=None,
    strand=None,
    spliced_transcripts=None,
    seq=None,
    is_best_transcript=False,
):

Args

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

mavis.annotate.genomic.PreTranscript.generate_splicing_patterns()

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

def generate_splicing_patterns(self):

Returns

  • List[SplicingPattern]: List of positions to be spliced together

Note

see theory - predicting splicing patterns

mavis.annotate.genomic.PreTranscript.gene()

Gene: the gene this transcript belongs to

@property
def gene(self):

Args

  • self

mavis.annotate.genomic.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, splicing_pattern, stick_direction=None, allow_outside=True
):

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

mavis.annotate.genomic.PreTranscript.exon_number()

exon numbering is based on the direction of translation

def exon_number(self, exon):

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

mavis.annotate.genomic.PreTranscript.translations()

List[mavis.annotate.protein.Translation]: list of translations associated with this transcript

@property
def translations(self):

Args

  • self

mavis.annotate.genomic.PreTranscript.transcripts()

List[Transcript]: list of spliced transcripts

@property
def transcripts(self):

Args

  • self

class mavis.annotate.genomic.Transcript

inherits BioInterval

mavis.annotate.genomic.Transcript.__init__()

splicing pattern is given in genomic coordinates

def __init__(self, pre_transcript, splicing_patt, seq=None, translations=None):

Args

  • pre_transcript (PreTranscript): the unspliced transcript
  • splicing_patt (List[int]): the list of splicing positions
  • seq (str): the cdna sequence

mavis.annotate.genomic.Transcript.unspliced_transcript()

PreTranscript: the unspliced transcript this splice variant belongs to

@property
def unspliced_transcript(self):

Args

  • self