seqann models¶
Annotation¶
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class
seqann.models.annotation.
Annotation
(missing: Dict[KT, VT] = None, ambig: Dict[KT, VT] = None, seq: Bio.SeqRecord.SeqRecord = None, features: Dict[KT, VT] = None, covered: int = None, annotation: Dict[KT, VT] = {}, blocks: List[List[int]] = None, method: str = None, mapping: Dict[KT, VT] = None, refmissing: List[str] = None, exact_match: List[str] = None, exact: bool = False, structure: List[seqann.feature_client.models.feature.Feature] = None, complete_annotation: bool = False, gfe: str = None)[source]¶ Bases:
seqann.models.base_model_.Model
classdocs
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classmethod
from_dict
(dikt) → seqann.models.annotation.Annotation[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The Annotation of this Annotation. Return type: Annotation
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complete_annotation
¶ Gets the complete_annotation of this Annotation.
Returns: The complete_annotation of this Annotation. Return type: bool
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exact
¶ Gets the exact of this Annotation.
Returns: The exact of this Annotation. Return type: bool
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features
¶ Gets the features of this Annotation.
Returns: The features of this Annotation. Return type: Dict
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structure
¶ Gets the structure of this Annotation.
Returns: The structure of this Annotation. Return type: List[Feature]
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covered
¶ Gets the coverage of this Annotation.
Returns: The covered of this Annotation. Return type: int
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seq
¶ Gets the coverage of this Annotation.
Returns: The seq of this Annotation. Return type: SeqRecord
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ambig
¶ Gets the ambig of this Annotation.
Returns: The ambig of this Annotation. Return type: Dict
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method
¶ Gets the method of this Annotation.
Returns: The method of this Annotation. Return type: str
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missing
¶ Gets the missing of this Annotation.
Returns: The missing of this Annotation. Return type: Dict
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mapping
¶ Gets the coverage of this Annotation.
Returns: The seq of this Annotation. Return type: Dict
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refmissing
¶ Gets the refmissing of this Annotation.
Returns: The refmissing of this Annotation. Return type: List[str]
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exact_match
¶ Gets the exact_match of this Annotation.
Returns: The exact_match of this Annotation. Return type: List[str]
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annotation
¶ Gets the coverage of this Annotation.
Returns: The seq of this Annotation. Return type: Dict
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blocks
¶ Gets the coverage of this Annotation.
Returns: The blocks of this Annotation. Return type: List[List[int]]
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gfe
¶ Gets the coverage of this Annotation.
Returns: The gfe of this Annotation. Return type: Dict
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aligned
¶ Gets the coverage of this Annotation.
Returns: The aligned of this Annotation. Return type: Dict
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classmethod
Reference Data¶
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class
seqann.models.reference_data.
ReferenceData
(server: <module 'BioSQL.BioSeqDatabase' from '/home/docs/checkouts/readthedocs.org/user_builds/seqann/envs/latest/lib/python3.7/site-packages/BioSQL/BioSeqDatabase.py'> = None, datafile: str = None, dbversion: str = '3310', alleles: List[T] = None, seqdata: Dict[KT, VT] = None, hladata: Dict[KT, VT] = None, featuredata=None, kir: bool = False, alignments: bool = False, verbose: bool = False, verbosity: int = 0)[source]¶ Bases:
seqann.models.base_model_.Model
classdocs
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classmethod
from_dict
(dikt) → seqann.models.reference_data.ReferenceData[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The ReferenceData of this ReferenceData. Return type: ReferenceData
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server
¶ Gets the server of this ReferenceData.
Returns: The server of this ReferenceData. Return type: BioSeqDatabase
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verbose
¶ Gets the server of this ReferenceData.
Returns: The server of this ReferenceData. Return type: BioSeqDatabase
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verbosity
¶ Gets the server of this ReferenceData.
Returns: The server of this ReferenceData. Return type: BioSeqDatabase
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alignments
¶ Gets the alignments of this ReferenceData.
Returns: The alignments of this ReferenceData. Return type: BioSeqDatabase
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datafile
¶ Gets the datafile of this ReferenceData.
Returns: The datafile of this ReferenceData. Return type: str
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dbversion
¶ Gets the dbversion of this ReferenceData.
Returns: The dbversion of this ReferenceData. Return type: str
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structures
¶ Gets the structures of this ReferenceData.
Returns: The structures of this ReferenceData. Return type: Dict
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structure_max
¶ Gets the structure_max of this ReferenceData.
Returns: The structure_max of this ReferenceData. Return type: Dict
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hlaref
¶ Gets the hlaref of this ReferenceData.
Returns: The hlaref of this ReferenceData. Return type: Dict
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seqref
¶ Gets the seqref of this ReferenceData.
Returns: The seqref of this ReferenceData. Return type: Dict
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blastdb
¶ Gets the blastdb of this ReferenceData.
Returns: The blastdb of this ReferenceData. Return type: str
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struct_order
¶ Gets the struct_order of this ReferenceData.
Returns: The struct_order of this ReferenceData. Return type: Dict
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feature_lengths
¶ Gets the feature_lengths of this ReferenceData.
Returns: The feature_lengths of this ReferenceData. Return type: Dict
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hla_names
¶ Gets the hla_names of this ReferenceData.
Returns: The hla_names of this ReferenceData. Return type: Dict
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kir
¶ Gets the kir of this ReferenceData.
Returns: The kir of this ReferenceData. Return type: bool
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hla_loci
¶ Gets the hla_loci of this ReferenceData.
Returns: The hla_loci of this ReferenceData. Return type: List[str]
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server_avail
¶ Gets the server_avail of this ReferenceData.
Returns: The server_avail of this ReferenceData. Return type: bool
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search_refdata
(seq, locus)[source]¶ This checks to see if a sequence already exists in the reference data. If it does, then it’ll return the known annotation.
Returns: The Annotation of associated with the input sequence Return type: Annotation Example:
>>> from Bio.Seq import Seq >>> from seqann.models.reference_data import ReferenceData >>> sequence = Seq('AGAGACTCTCCCGAGGATTTCGTGTACCAGTTTAAGGCCATGTGCTACTTCACC') >>> refdata = ReferenceData() >>> matched_annotation = refdata.search_refdata(sequence, locus)
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seqrecord
(allele, locus)[source]¶ Gets the Annotation from the found sequence
Returns: The Annotation from the found sequence Return type: Annotation
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seqannotation
(seqrecord, allele, loc)[source]¶ Gets the Annotation from the found sequence
Returns: The Annotation from the found sequence Return type: Annotation
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classmethod
Blast¶
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class
seqann.models.blast.
Blast
(failed: bool = None, match_seqs: List[BioSQL.BioSeq.DBSeqRecord] = None, alleles: List[str] = None)[source]¶ Bases:
seqann.models.base_model_.Model
classdocs
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classmethod
from_dict
(dikt) → seqann.models.blast.Blast[source]¶ Returns the dict as a model
Parameters: dikt – A dict. Type: dict Returns: The Blast of this Blast. Return type: Blast
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match_seqs
¶ Gets the match_seqs of this Blast.
Returns: The match_seqs of this Blast. Return type: List[str]
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alleles
¶ Gets the alleles of this Blast.
Returns: The alleles of this Blast. Return type: List[str]
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failed
¶ Gets the failed of this Blast.
Returns: The failed of this Blast. Return type: bool
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classmethod