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):
MetadataLogger.__init__(self)
allele = name.split("-")[-1].replace("H-2-", "")
self.organism = "H-2"
self.name = allele
self.prob = prob
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])
