seqann models¶

seqann models

Annotation¶

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

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

complete_annotation¶

Gets the complete_annotation of this Annotation.

Returns:	The complete_annotation of this Annotation.
Return type:	bool

exact¶

Gets the exact of this Annotation.

Returns:	The exact of this Annotation.
Return type:	bool

features¶

Gets the features of this Annotation.

Returns:	The features of this Annotation.
Return type:	Dict

structure¶

Gets the structure of this Annotation.

Returns:	The structure of this Annotation.
Return type:	List[Feature]

covered¶

Gets the coverage of this Annotation.

Returns:	The covered of this Annotation.
Return type:	int

seq¶

Gets the coverage of this Annotation.

Returns:	The seq of this Annotation.
Return type:	SeqRecord

ambig¶

Gets the ambig of this Annotation.

Returns:	The ambig of this Annotation.
Return type:	Dict

method¶

Gets the method of this Annotation.

Returns:	The method of this Annotation.
Return type:	str

missing¶

Gets the missing of this Annotation.

Returns:	The missing of this Annotation.
Return type:	Dict

mapping¶

Gets the coverage of this Annotation.

Returns:	The seq of this Annotation.
Return type:	Dict

refmissing¶

Gets the refmissing of this Annotation.

Returns:	The refmissing of this Annotation.
Return type:	List[str]

exact_match¶

Gets the exact_match of this Annotation.

Returns:	The exact_match of this Annotation.
Return type:	List[str]

annotation¶

Gets the coverage of this Annotation.

Returns:	The seq of this Annotation.
Return type:	Dict

blocks¶

Gets the coverage of this Annotation.

Returns:	The blocks of this Annotation.
Return type:	List[List[int]]

gfe¶

Gets the coverage of this Annotation.

Returns:	The gfe of this Annotation.
Return type:	Dict

aligned¶

Gets the coverage of this Annotation.

Returns:	The aligned of this Annotation.
Return type:	Dict

check_annotation()[source]¶

clean()[source]¶

Reference Data¶

seqann.models.reference_data.download_dat(url, dat)[source]¶

class seqann.models.reference_data.ReferenceData(server: <module 'BioSQL.BioSeqDatabase' from '/home/docs/checkouts/readthedocs.org/user_builds/seqann/envs/stable/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

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

server¶

Gets the server of this ReferenceData.

Returns:	The server of this ReferenceData.
Return type:	BioSeqDatabase

verbose¶

Gets the server of this ReferenceData.

Returns:	The server of this ReferenceData.
Return type:	BioSeqDatabase

verbosity¶

Gets the server of this ReferenceData.

Returns:	The server of this ReferenceData.
Return type:	BioSeqDatabase

alignments¶

Gets the alignments of this ReferenceData.

Returns:	The alignments of this ReferenceData.
Return type:	BioSeqDatabase

datafile¶

Gets the datafile of this ReferenceData.

Returns:	The datafile of this ReferenceData.
Return type:	str

dbversion¶

Gets the dbversion of this ReferenceData.

Returns:	The dbversion of this ReferenceData.
Return type:	str

structures¶

Gets the structures of this ReferenceData.

Returns:	The structures of this ReferenceData.
Return type:	Dict

structure_max¶

Gets the structure_max of this ReferenceData.

Returns:	The structure_max of this ReferenceData.
Return type:	Dict

hlaref¶

Gets the hlaref of this ReferenceData.

Returns:	The hlaref of this ReferenceData.
Return type:	Dict

seqref¶

Gets the seqref of this ReferenceData.

Returns:	The seqref of this ReferenceData.
Return type:	Dict

blastdb¶

Gets the blastdb of this ReferenceData.

Returns:	The blastdb of this ReferenceData.
Return type:	str

struct_order¶

Gets the struct_order of this ReferenceData.

Returns:	The struct_order of this ReferenceData.
Return type:	Dict

feature_lengths¶

Gets the feature_lengths of this ReferenceData.

Returns:	The feature_lengths of this ReferenceData.
Return type:	Dict

hla_names¶

Gets the hla_names of this ReferenceData.

Returns:	The hla_names of this ReferenceData.
Return type:	Dict

kir¶

Gets the kir of this ReferenceData.

Returns:	The kir of this ReferenceData.
Return type:	bool

hla_loci¶

Gets the hla_loci of this ReferenceData.

Returns:	The hla_loci of this ReferenceData.
Return type:	List[str]

server_avail¶

Gets the server_avail of this ReferenceData.

Returns:	The server_avail of this ReferenceData.
Return type:	bool

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)

seqrecord(allele, locus)[source]¶

Gets the Annotation from the found sequence

Returns:	The Annotation from the found sequence
Return type:	Annotation

seqannotation(seqrecord, allele, loc)[source]¶

Gets the Annotation from the found sequence

Returns:	The Annotation from the found sequence
Return type:	Annotation

Blast¶

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

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

match_seqs¶

Gets the match_seqs of this Blast.

Returns:	The match_seqs of this Blast.
Return type:	List[str]

alleles¶

Gets the alleles of this Blast.

Returns:	The alleles of this Blast.
Return type:	List[str]

failed¶

Gets the failed of this Blast.

Returns:	The failed of this Blast.
Return type:	bool