def __init__(self, id, type, chrom, genomePos, ref, obs, coding, isHomozygous, isSynonymous, experimentalDesign=None, metadata=None): """ Constructor for a variant, see init-types in class parameters :param str id: :class:`~Fred2.Core.Variant.Variant` id :param type: An Enum type of the :class:`~Fred2.Core.Variant.Variant` either SNP, DEL, or INS :type type: :func:`~Fred2.Core.Variant.VariationType` :param str chrom: The chromosome on which the variant lies :param int genomePos: The genomic position of the :class:`~Fred2.Core.Variant.Variant` :param str ref: The reference seq at the genomic position :param str obs: The observed variation at the genomic position :param coding: A dictionary of associated transcripts. Key=transcript_id, value=:class:`~Fred2.Core.Variant.MutationSyntax` :type coding: dict(str,:class:`~Fred2.Core.Variant.MutationSyntax`) :param bool isHomozygous: Defines if variant is homozygous or not :param bool isSynonymous: Defines if variant is a synonymous mutation or not :param str experimentalDesign: String specifying the experimental condition (e.g. tumor) :param dict(list) metadata: meta information (not relevant for core functionality of Fred2) """ MetadataLogger.__init__(self) self.id = id self.type = type self.chrom = chrom self.genomePos = genomePos self.ref = ref.upper() self.obs = obs.upper() self.isHomozygous = isHomozygous self.isSynonymous = isSynonymous self.coding = coding # dict transcript_id:MutationSyntax self.experimentalDesign = "" if experimentalDesign is None else experimentalDesign if metadata is not None: for meta in metadata: self.log_metadata(meta, metadata[meta])
def __init__(self, name, prob=None): MetadataLogger.__init__(self) allele = name.split("-")[-1].replace("H-2-", "") self.organism = "H-2" self.name = allele self.prob = prob
def __init__(self, _seq, gene_id="unknown", transcript_id=None, orig_transcript=None, vars=None): """ :param str _seq: String of an IUPACProtein alphabet, representing the protein :param str gene_id: ID of the genome the protein originated from :param str transcript_id: ID of the transcript the protein originated from :param orig_transcript: Reference to the originating transcript object :type orig_transcript: :class:`~Fred2.Core.Transcript.Transcript` :param vars: Nonsynonymous variants that are associated with the protein. key=position within protein, value=list of variants at that pos :type vars: dict(int,list(:class:`~Fred2.Core.Variant.Variant`)) """ # Init parent type: MetadataLogger.__init__(self) Seq.__init__(self, _seq.upper(), IUPAC.IUPACProtein) # Init own member: if vars is None: self.vars = dict() else: self.vars = vars # {prot-position: list(variant)} self.orig_transcript = orig_transcript self.transcript_id = "Protein_%i" % Protein.newid( ) if transcript_id is None else transcript_id self.gene_id = gene_id
def __init__(self, _seq, _gene_id="unknown", _transcript_id=None, _orig_transcript=None, _vars=None): """ :param str _seq: String of an IUPACProtein alphabet, representing the protein :param str _gene_id: ID of the genome the protein originated from :param str _transcript_id: ID of the transcript the protein originated from :param Transcript _orig_transcript: Reference to the originating transcript :param dict(int,list(Variant)) _vars: Nonsynonymous variants that are assoziated with the protein. key=position within protein, value=list of variants at that pos """ # Init parent type: MetadataLogger.__init__(self) Seq.__init__(self, _seq.upper(), IUPAC.IUPACProtein) # Init own member: if _vars is None: self.vars = dict() else: self.vars = _vars # {prot-position: list(variant)} self.orig_transcript = _orig_transcript self.transcript_id = "Protein_%i"%Protein.newid() if _transcript_id is None else _transcript_id self.gene_id = _gene_id
def __init__(self, _name, prob=None): """ :param str _name: input name in new nomenclature (A*01:01) """ MetadataLogger.__init__(self) name = _name.split("-")[-1].replace("HLA-", "") self.name = name self.locus, rest = name.split('*') self.supertype, self.subtype = rest.split(':')[:2] self.prob = prob
def __init__(self, _seq, proteins=None, vars=None, transcripts=None): """ :param str _seq: sequence of the peptide in one letter amino acid code """ MetadataLogger.__init__(self) Seq.__init__(self, _seq, IUPAC.IUPACProtein) self.proteins = {} if proteins is None else proteins self.vars = {} if vars is None else vars self.transcripts = {} if transcripts is None else transcripts
def __init__(self, name, prob=None): """ :param str name: input name in new nomenclature (A*01:01) :param float prob: optional population frequency of allele in [0,1] """ MetadataLogger.__init__(self) name = name.split("-")[-1].replace("HLA-", "") self.name = name self.locus, rest = name.split('*') self.supertype, self.subtype = rest.split(':')[:2] self.prob = prob
def __init__(self, _seq, _gene_id="unknown", _transcript_id=None, _vars=None): """ :param str _gene_id: input genome ID :param str _transcript_id: input transcript RefSeqID :param str _seq: Transcript RefSeq sequence :param dict(int,Variant) _vars: a dict of transcript position to Variant that is specific to the transcript. """ MetadataLogger.__init__(self) Seq.__init__(self, _seq.upper(), generic_rna) self.gene_id = _gene_id self.transcript_id = Transcript.newid() if _transcript_id is None else _transcript_id #TODO: this is not what the doc string says: self.vars = dict() if _vars is None else _vars
def __init__(self, seq, gene_id="unknown", transcript_id=None, vars=None): """ :param str gene_id: Genome ID :param str transcript_id: :class:`~Fred2.Core.Transcript.Transcript` RefSeqID :param str seq: :class:`~Fred2.Core.Transcript.Transcript` sequence :param vars: A dict of :class:`~Fred2.Core.Transcript.Transcript` position to :class:`Fred2.Core.Variant.Variant` that is specific to the :class:`~Fred2.Core.Transcript.Transcript` :type vars: dict(int,:class:`Fred2.Core.Variant.Variant`) """ MetadataLogger.__init__(self) Seq.__init__(self, seq.upper(), generic_rna) self.gene_id = gene_id self.transcript_id = Transcript.newid() if transcript_id is None else transcript_id self.vars = dict() if vars is None else vars
def __init__(self, seq, gene_id="unknown", transcript_id=None, vars=None): """ :param str gene_id: Genome ID :param str transcript_id: :class:`~Fred2.Core.Transcript.Transcript` RefSeqID :param str seq: :class:`~Fred2.Core.Transcript.Transcript` sequence :param vars: A dict of :class:`~Fred2.Core.Transcript.Transcript` position to :class:`Fred2.Core.Variant.Variant` that is specific to the :class:`~Fred2.Core.Transcript.Transcript` :type vars: dict(int,:class:`Fred2.Core.Variant.Variant`) """ MetadataLogger.__init__(self) Seq.__init__(self, seq.upper(), generic_rna) self.gene_id = gene_id self.transcript_id = Transcript.newid( ) if transcript_id is None else transcript_id self.vars = dict() if vars is None else vars
def __init__(self, name, prob=None): """ :param str name: input name in new nomenclature (DPA1*01:03-DPB1*01:01) :param float prob: optional population frequency of allele in [0,1] """ MetadataLogger.__init__(self) alpha_chain = name.replace("HLA-", "").split("-")[0] beta_chain = name.replace("HLA-", "").split("-")[1] name = alpha_chain+"-"+beta_chain self.name = name self.alpha_chain = alpha_chain self.beta_chain = beta_chain self.alpha_locus, alpha_rest = self.alpha_chain.split('*') self.alpha_supertype, self.alpha_subtype = alpha_rest.split(':')[:2] self.beta_locus, beta_rest = self.beta_chain.split('*') self.beta_supertype, self.beta_subtype = beta_rest.split(':')[:2] self.prob = prob
def __init__(self, _seq, _gene_id="unknown", _transcript_id=None, _vars=None): """ :param str _gene_id: input genome ID :param str _transcript_id: input transcript RefSeqID :param str _seq: Transcript RefSeq sequence :param dict(int,Variant) _vars: Dict of Variants for specific positions in the transcript. key=position, value=Variant """ MetadataLogger.__init__(self) Seq.__init__(self, _seq, generic_rna) self.gene_id = _gene_id self.transcript_id = Transcript.newid() if _transcript_id is None else _transcript_id if _vars is not None: self.vars = {v.get_transcript_position(_transcript_id): v \ for v in _vars} else: self.vars = dict()
def __init__(self, id, type, chrom, genomePos, ref, obs, coding, isHomozygous, isSynonymous, experimentalDesign=None, metadata=None): """ Constructor for a variant, see init-types in class parameters """ MetadataLogger.__init__(self) self.id = id self.type = type self.chrom = chrom self.genomePos = genomePos self.ref = ref.upper() self.obs = obs.upper() self.gene = None self.isHomozygous = isHomozygous self.isSynonymous = isSynonymous self.coding = coding # dict transcript_id:MutationSyntax self.experimentalDesign = "" if experimentalDesign is None else experimentalDesign if metadata is not None: for meta in metadata: self.log_metadata(meta, metadata[meta])
def __init__(self, _seq, gene_id="unknown", transcript_id=None, orig_transcript=None, vars=None): """ :param str _seq: String of an IUPACProtein alphabet, representing the protein :param str gene_id: ID of the genome the protein originated from :param str transcript_id: ID of the transcript the protein originated from :param orig_transcript: Reference to the originating transcript object :type orig_transcript: :class:`~Fred2.Core.Transcript.Transcript` :param vars: Nonsynonymous variants that are associated with the protein. key=position within protein, value=list of variants at that pos :type vars: dict(int,list(:class:`~Fred2.Core.Variant.Variant`)) """ # Init parent type: MetadataLogger.__init__(self) Seq.__init__(self, _seq.upper(), IUPAC.IUPACProtein) # Init own member: if vars is None: self.vars = dict() else: self.vars = vars # {prot-position: list(variant)} self.orig_transcript = orig_transcript self.transcript_id = "Protein_%i"%Protein.newid() if transcript_id is None else transcript_id self.gene_id = gene_id
def __init__(self, id, type, chrom, genomePos, ref, obs, coding, isHomozygous, isSynonymous, experimentalDesign=None, metadata=None): """ Constructor for a variant, see init-types in class parameters :param str id: :class:`~Fred2.Core.Variant.Variant` id :param type: An Enum type of the :class:`~Fred2.Core.Variant.Variant` either SNP, DEL, or INS :type type: :func:`~Fred2.Core.Variant.VariationType` :param str chrom: The chromosome on which the variant lies :param int genomePos: The genomic position of the :class:`~Fred2.Core.Variant.Variant` :param str ref: The reference seq at the genomic position :param str obs: The observed variation at the genomic position :param coding: A dictionary of associated transcripts. Key=transcript_id, value=:class:`~Fred2.Core.Variant.MutationSyntax` :type coding: dict(str,:class:`~Fred2.Core.Variant.MutationSyntax`) :param bool isHomozygous: Defines if variant is homozygous or not :param bool isSynonymous: Defines if variant is a synonymous mutation or not :param str experimentalDesign: String specifying the experimental condition (e.g. tumor) :param dict(list) metadata: meta information (not relevant for core functionality of Fred2) """ MetadataLogger.__init__(self) self.id = id self.type = type self.chrom = chrom self.genomePos = genomePos self.ref = ref.upper() self.obs = obs.upper() self.gene = None self.isHomozygous = isHomozygous self.isSynonymous = isSynonymous self.coding = coding # dict transcript_id:MutationSyntax self.experimentalDesign = "" if experimentalDesign is None else experimentalDesign if metadata is not None: for meta in metadata: self.log_metadata(meta, metadata[meta])