protein module

class mavis.annotate.protein.Domain(name, regions, translation=None, data=None)

Bases: object

Parameters:

• name (str) – the name of the domain i.e. PF00876
• regions (list of DomainRegion) – the amino acid ranges that are part of the domain
• transcript (Transcript) – the ‘parent’ transcript this domain belongs to

Raises:

AttributeError – if the end of any region is less than the start

Example

>>> Domain('DNA binding domain', [(1, 4), (10, 24)], transcript)

align_seq(input_sequence, REFERENCE_GENOME=None)

align each region to the input sequence starting with the last one. then take the subset of sequence that remains to align the second last and so on return a list of intervals for the alignment. If multiple alignments are found, then raise an error

Parameters:

• input_sequence (str) – the sequence to be aligned to
• REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name

Returns:

tuple contains

• int: the number of matches
• int: the total number of amino acids to be aligned
• list of DomainRegion: the list of domain regions on the new input sequence

Return type:

tuple

Raises:

• AttributeError – if sequence information is not available
• UserWarning – if a valid alignment could not be found or no best alignment was found

get_seqs(REFERENCE_GENOME=None, ignore_cache=False)

returns the amino acid sequences for each of the domain regions associated with this domain in the order of the regions (sorted by start)

Parameters:REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name Returns:list of amino acid sequences for each DomainRegion Return type:list of str Raises:AttributeError – if there is not enough sequence information given to determine this

key()

tuple: a tuple representing the items expected to be unique. for hashing and comparing

score_region_mapping(REFERENCE_GENOME=None)

compares the sequence in each DomainRegion to the sequence collected for that domain region from the translation object

Parameters:REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name Returns:tuple contains

• int: the number of matching amino acids
• int: the total number of amino acids

Return type:tuple of int and int

translation

Translation – the Translation this domain belongs to

class mavis.annotate.protein.DomainRegion(start, end, seq=None, domain=None, name=None)

Bases: mavis.annotate.base.BioInterval

class mavis.annotate.protein.Translation(start, end, transcript=None, domains=None, seq=None, name=None)

Bases: mavis.annotate.base.BioInterval

describes the splicing pattern and cds start and end with reference to a particular transcript

Parameters:

• start (int) – start of the coding sequence (cds) relative to the start of the first exon in the transcript
• end (int) – end of the coding sequence (cds) relative to the start of the first exon in the transcript
• transcript (Transcript) – the transcript this is a Translation of
• domains (list of Domain) – a list of the domains on this translation
• sequence (str) – the cds sequence

convert_aa_to_cdna(pos)

Parameters:pos (int) – the amino acid position Returns:the cdna equivalent (with CODON_SIZE uncertainty) Return type:Interval

convert_cdna_to_aa(pos)

Parameters:pos (int) – the cdna position Returns:the protein/amino-acid position Return type:int Raises:AttributeError – the cdna position is not translated

convert_genomic_to_cds(pos)

converts a genomic position to its cds (coding sequence) equivalent

Parameters:pos (int) – the genomic position Returns:the cds position (negative if before the initiation start site) Return type:int

convert_genomic_to_cds_notation(pos)

converts a genomic position to its cds (coding sequence) equivalent using hgvs cds notation

Parameters:pos (int) – the genomic position Returns:the cds position notation Return type:str

Example

>>> tl = Translation(...)
# a position before the translation start
>>> tl.convert_genomic_to_cds_notation(1010)
'-50'
# a position after the translation end
>>> tl.convert_genomic_to_cds_notation(2031)
'*72'
# an intronic position
>>> tl.convert_genomic_to_cds_notation(1542)
'50+10'
>>> tl.convert_genomic_to_cds_notation(1589)
'51-14'

convert_genomic_to_nearest_cds(pos)

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

Parameters:pos (int) – the genomic position Returns:

• int - the cds position
• int - the intronic shift

Return type:tuple of int and int

get_AA_seq(REFERENCE_GENOME=None, ignore_cache=False)

Parameters:REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name Returns:the amino acid sequence Return type:str Raises:AttributeError – if the reference sequence has not been given and is not set

get_cds_seq(REFERENCE_GENOME=None, ignore_cache=False)

Parameters:REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name Returns:the cds sequence Return type:str Raises:AttributeError – if the reference sequence has not been given and is not set

get_seq(REFERENCE_GENOME=None, ignore_cache=False)

wrapper for the sequence method

Parameters:REFERENCE_GENOME (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name

key()

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

transcript

Transcript – the spliced transcript this translation belongs to

mavis.annotate.protein.calculate_ORF(spliced_cdna_sequence, min_orf_size=None)

calculate all possible open reading frames given a spliced cdna sequence (no introns)

Parameters:spliced_cdna_sequence (str) – the sequence Returns:list of open reading frame positions on the input sequence Return type:list of Interval