genomic module

class mavis.annotate.genomic.Exon(start, end, transcript=None, name=None, intact_start_splice=True, intact_end_splice=True, seq=None)

Bases: mavis.annotate.base.BioInterval

Parameters:

• start (int) – the genomic start position
• end (int) – the genomic end position
• name (str) – the name of the exon
• transcript (usTranscript) – the ‘parent’ transcript this exon belongs to
• intact_start_splice (bool) – if the starting splice site has been abrogated
• intact_end_splice (bool) – if the end splice site has been abrogated

Raises:

AttributeError – if the exon start > the exon end

Example

>>> Exon(15, 78)

acceptor

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

acceptor_splice_site

Interval – the genomic range describing the splice site

donor

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

donor_splice_site

Interval – the genomic range describing the splice site

end_splice_site

Interval – the genomic range describing the splice site

start_splice_site

Interval – the genomic range describing the splice site

transcript

usTranscript – the transcript this exon belongs to

class mavis.annotate.genomic.Gene(chr, start, end, name=None, strand='?', aliases=None, seq=None)

Bases: mavis.annotate.base.BioInterval

Parameters:

• chr (str) – the chromosome
• name (str) – the gene name/id i.e. ENSG0001
• strand (STRAND) – the genomic strand ‘+’ or ‘-‘
• aliases (list of str) – a list of aliases. For example the hugo name could go here
• seq (str) – genomic seq of the gene

Example

>>> Gene('X', 1, 1000, 'ENG0001', '+', ['KRAS'])

chr

returns the name of the chromosome that this gene resides on

get_seq(REFERENCE_GENOME, ignore_cache=False)

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

Parameters:

• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – 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:

the sequence of the gene

Return type:

str

key()

see structural_variant.annotate.base.BioInterval.key()

spliced_transcripts

list of Transcript – list of transcripts

to_dict()

see structural_variant.annotate.base.BioInterval.to_dict()

transcript_priority(transcript)

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

Warning

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

transcripts

list of usTranscript – list of unspliced transcripts

translations

list of Translation – list of translations

class mavis.annotate.genomic.IntergenicRegion(chr, start, end, strand)

Bases: mavis.annotate.base.BioInterval

Parameters:

• chr (str) – the reference object/chromosome for this region
• start (int) – the start of the IntergenicRegion
• end (int) – the end of the IntergenicRegion
• strand (STRAND) – the strand the region is defined on

Example

>>> IntergenicRegion('1', 1, 100, '+')

chr

returns the name of the chromosome that this gene resides on

key()

see structural_variant.annotate.base.BioInterval.key()

to_dict()

see structural_variant.annotate.base.BioInterval.to_dict()

class mavis.annotate.genomic.SplicingPattern(*args, splice_type='normal')

Bases: list

class mavis.annotate.genomic.Template(name, start, end, seq=None, bands=None)

Bases: mavis.annotate.base.BioInterval

class mavis.annotate.genomic.Transcript(ust, splicing_patt, seq=None, translations=None)

Bases: mavis.annotate.base.BioInterval

splicing pattern is given in genomic coordinates

Parameters:

• us_transcript (usTranscript) – the unspliced transcript
• splicing_patt (list of int) – the list of splicing positions
• seq (str) – the cdna sequence
• translations (list of Translation) – the list of translations of this transcript

convert_cdna_to_genomic(pos)

Parameters:pos (int) – cdna position Returns:the genomic equivalent Return type:int

convert_genomic_to_cdna(pos)

Parameters:pos (int) – the genomic position to be converted Returns:the cdna equivalent Return type:int Raises:IndexError – when a genomic position not present in the cdna is attempted to be converted

convert_genomic_to_nearest_cdna(pos)

get_seq(REFERENCE_GENOME=None, ignore_cache=False)

Parameters:

• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – 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:

the sequence corresponding to the spliced cdna

Return type:

str

unspliced_transcript

usTranscript – the unspliced transcript this splice variant belongs to

class mavis.annotate.genomic.usTranscript(exons, gene=None, name=None, strand=None, spliced_transcripts=None, seq=None, is_best_transcript=False)

Bases: mavis.annotate.base.BioInterval

creates a new transcript object

Parameters:

• exons (list of Exon) – list of Exon that make up the transcript
• genomic_start (int) – genomic start position of the transcript
• genomic_end (int) – genomic end position of 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
• seq (str) – unspliced cDNA seq

convert_cdna_to_genomic(pos, splicing_pattern)

Parameters:

• pos (int) – cdna position
• splicing_pattern (SplicingPattern) – list of genomic splice sites 3‘5’ repeating

Returns:

the genomic equivalent

Return type:

int

convert_genomic_to_cdna(pos, splicing_pattern)

Parameters:

• pos (int) – the genomic position to be converted
• splicing_pattern (SplicingPattern) – list of genomic splice sites 3‘5’ repeating

Returns:

the cdna equivalent

Return type:

int

Raises:

IndexError – when a genomic position not present in the cdna is attempted to be converted

convert_genomic_to_nearest_cdna(pos, splicing_pattern)

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

Parameters:

• pos (int) – the genomic position
• splicing_pattern (SplicingPattern) – the splicing pattern

Returns:

• int - the exonic cdna position
• int - the intronic shift

Return type:

tuple of int and int

exon_number(exon)

exon numbering is based on the direction of translation

Parameters:exon (Exon) – the exon to be numbered Returns:the exon number (1 based) Return type:int Raises:AttributeError – if the strand is not given or the exon does not belong to the transcript

gene

Gene – the gene this transcript belongs to

generate_splicing_patterns()

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

Returns:List of positions to be spliced together Return type:list of SplicingPattern

see theory - predicting splicing patterns

get_cdna_seq(splicing_pattern, REFERENCE_GENOME=None, ignore_cache=False)

Parameters:

• splicing_pattern (SplicingPattern) – the list of splicing positions
• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – 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:

the spliced cDNA sequence

Return type:

str

get_seq(REFERENCE_GENOME=None, ignore_cache=False)

Parameters:

• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – 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:

the sequence of the transcript including introns (but relative to strand)

Return type:

str

transcripts

list of Transcript – list of spliced transcripts

translations

list of Translation – list of translations associated with this transcript