pyhml package¶

pyhml¶

class pyhml.pyhml.HmlParser(hmlversion: str = None, verbose: bool = False)[source]¶

Bases: object

A python HML parser that converts any valid HML file into an python object. Allows users to easily interact with HML data as python objects. Users can also easily convert the HML data to a pandas DataFrame. If no hmlversion is provided, then the schemas for all HML versions are loaded.

Examples:

>>> import pyhml
>>> hmlparser = pyhml.HmlParser(verbose=True)
>>> hml = hmlparser.parse(hml_file)
>>> hml_df = hml.toPandas()

Parameters:	hmlversion (str) – A specific HML version to load. verbose (bool) – Flag for running in verbose.

parse(hml_file: str) → pyhml.models.hml.HML[source]¶

Parses an HML file into a python object.

>>> hml = hmlparser.parse(hml_file)

Parameters:	hml_file – A valid HML file
Type:	str
Returns:	Object containing HML data
Return type:	HML

Data Objects¶

HML¶

class pyhml.models.hml.HML(project_name: str = None, version: str = None, schema_location: str = None, reporting_center: pyhml.models.reporting_center.ReportingCenter = None, sample: List[pyhml.models.sample.Sample] = None)[source]¶

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

classmethod from_dict(dikt) → pyhml.models.hml.HML[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The HML of this HML.
Return type:	HML

project_name¶

Gets the project_name of this HML.

Returns:	The project_name of this HML.
Return type:	str

reporting_center¶

Gets the reporting_center of this HML.

Returns:	The reporting_center of this HML.
Return type:	ReportingCenter

sample¶

Gets the sample of this HML.

Returns:	The sample of this HML.
Return type:	List[Sample]

schema_location¶

Gets the schema_location of this HML.

Returns:	The schema_location of this HML.
Return type:	str

toPandas() → pandas.core.frame.DataFrame[source]¶

Returns all the HML data as a pandas DataFrame.

Examples:

>>> import pyhml
>>> hmlparser = pyhml.HmlParser(verbose=True)
>>> hml = hmlparser.parse(hml_file)
>>> hml_df = hml.toPandas()

Returns:	Pandas dataframe
Return type:	DataFrame

tobiotype(outdir, dtype='fasta', by='file')[source]¶

Converts an HML object to a BioPython data fromat

Examples:

>>> import pyhml
>>> hmlparser = pyhml.HmlParser(verbose=True)
>>> hml = hmlparser.parse(hml_file)
>>> hml.tobiotype("output/directory",dtype='imgt', by='subject')

Parameters:	outdir (str) – The output directory dtype – The BioPython output type by (str) – What to print out the HML file by

version¶

Gets the version of this HML.

Returns:	The version of this HML.
Return type:	str

Sample¶

class pyhml.models.sample.Sample(center_code: int = None, id: str = None, collection_method: str = None, typing: List[pyhml.models.typing.Typing] = None)[source]¶

Bases: pyhml.models.base_model_.Model

Examples:

>>> from pyhml.models.typing import Typing
>>> from pyhml.models.sample import Sample

center_code¶

Gets the center_code of this Sample.

Returns:	The center_code of this Sample.
Return type:	int

collection_method¶

Gets the collection_method of this Sample.

Returns:	The collection_method of this Sample.
Return type:	str

create_seqrecords()[source]¶

Creates the seq_records for this Sample.

classmethod from_dict(dikt) → pyhml.models.sample.Sample[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The Sample of this Sample.
Return type:	Sample

id¶

Gets the id of this Sample.

Returns:	The id of this Sample.
Return type:	str

seq_records¶

Gets the seq_records of this Sample.

Returns:	The seq_records of this Sample.
Return type:	Dict

typing¶

Gets the typing of this Sample.

Returns:	The typing of this Sample.
Return type:	List[Typing]

Typing¶

class pyhml.models.typing.Typing(date: str = None, gene_family: str = None, allele_assignment: List[pyhml.models.allele_assignment.AlleleAssignment] = None, consensus_sequence: List[pyhml.models.consensus.Consensus] = None, typing_method: pyhml.models.typing_method.TypingMethod = None)[source]¶

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

allele_assignment¶

Gets the allele_assignment of this Typing.

Returns:	The allele_assignment of this Typing.
Return type:	List[AlleleAssignment]

consensus_sequence¶

Gets the consensus_sequence of this Typing.

Returns:	The consensus_sequence of this Typing.
Return type:	List[Consensus]

create_seqrecord(subid)[source]¶

date¶

Gets the date of this Typing.

Returns:	The date of this Typing.
Return type:	str

classmethod from_dict(dikt) → pyhml.models.typing.Typing[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The Typing of this Typing.
Return type:	Typing

gene_family¶

Gets the gene_family of this Typing.

Returns:	The gene_family of this Typing.
Return type:	str

seq_records¶

Gets the seq_records of this ReferenceData.

Returns:	The seq_records of this ReferenceData.
Return type:	List[SeqRecord]

typing_method¶

Gets the typing_method of this Typing.

Returns:	The typing_method of this Typing.
Return type:	TypingMethod

Consensus¶

class pyhml.models.consensus.Consensus(date: str = None, consensus_sequence_block: List[pyhml.models.consensus_seq_block.ConsensusSeqBlock] = None, reference_database: List[pyhml.models.ref_database.RefDatabase] = None)[source]¶

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

consensus_sequence_block¶

Gets the consensus_sequence_block of this Consensus.

Returns:	The consensus_sequence_block of this Consensus.
Return type:	List[ConsensusSeqBlock]

date¶

Gets the date of this Consensus.

Returns:	The date of this Consensus.
Return type:	str

classmethod from_dict(dikt) → pyhml.models.consensus.Consensus[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The Consensus of this Consensus.
Return type:	Consensus

reference_database¶

Gets the reference_database of this Consensus.

Returns:	The reference_database of this Consensus.
Return type:	List[RefDatabase]

Consensus Block¶

class pyhml.models.consensus_seq_block.ConsensusSeqBlock(continuity: bool = None, description: str = None, end: int = None, expected_copy_number: int = None, phase_set: str = None, reference_sequence_id: str = None, start: int = None, strand: str = None, sequence: Bio.Seq.Seq = None, sequence_quality: List[pyhml.models.seq_quality.SeqQuality] = None, variant: List[pyhml.models.variant.Variant] = None)[source]¶

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

continuity¶

Gets the continuity of this ConsensusSeqBlock.

Returns:	The continuity of this ConsensusSeqBlock.
Return type:	bool

description¶

Gets the description of this ConsensusSeqBlock.

Returns:	The description of this ConsensusSeqBlock.
Return type:	str

end¶

Gets the end of this ConsensusSeqBlock.

Returns:	The end of this ConsensusSeqBlock.
Return type:	int

expected_copy_number¶

Gets the expected_copy_number of this ConsensusSeqBlock.

Returns:	The expected_copy_number of this ConsensusSeqBlock.
Return type:	int

classmethod from_dict(dikt) → pyhml.models.consensus_seq_block.ConsensusSeqBlock[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The ConsensusSeqBlock of this ConsensusSeqBlock.
Return type:	ConsensusSeqBlock

phase_set¶

Gets the phase_set of this ConsensusSeqBlock.

Returns:	The phase_set of this ConsensusSeqBlock.
Return type:	str

reference_sequence_id¶

Gets the reference_sequence_id of this ConsensusSeqBlock.

Returns:	The reference_sequence_id of this ConsensusSeqBlock.
Return type:	str

sequence¶

Gets the sequence of this ConsensusSeqBlock.

Returns:	The sequence of this ConsensusSeqBlock.
Return type:	Seq

sequence_quality¶

Gets the sequence_quality of this ConsensusSeqBlock.

Returns:	The sequence_quality of this ConsensusSeqBlock.
Return type:	List[SeqQuality]

start¶

Gets the start of this ConsensusSeqBlock.

Returns:	The start of this ConsensusSeqBlock.
Return type:	int

strand¶

Gets the strand of this ConsensusSeqBlock.

Returns:	The strand of this ConsensusSeqBlock.
Return type:	str

variant¶

Gets the variant of this ConsensusSeqBlock.

Returns:	The variant of this ConsensusSeqBlock.
Return type:	List[Variant]

Allele Assignment¶

class pyhml.models.allele_assignment.AlleleAssignment(allele_db: str = None, allele_version: str = None, date: str = None, glstring: List[str] = None, haploid: List[pyhml.models.haploid.Haploid] = None)[source]¶

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

allele_db¶

Gets the allele_db of this AlleleAssignment.

Returns:	The allele_db of this AlleleAssignment.
Return type:	str

allele_version¶

Gets the allele_version of this AlleleAssignment.

Returns:	The allele_version of this AlleleAssignment.
Return type:	str

date¶

Gets the date of this AlleleAssignment.

Returns:	The date of this AlleleAssignment.
Return type:	str

classmethod from_dict(dikt) → pyhml.models.allele_assignment.AlleleAssignment[source]¶

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The AlleleAssignment of this AlleleAssignment.
Return type:	AlleleAssignment

glstring¶

Gets the glstring of this AlleleAssignment.

Returns:	The glstring of this AlleleAssignment.
Return type:	List[str]

haploid¶

Gets the haploid of this AlleleAssignment.

Returns:	The haploid of this AlleleAssignment.
Return type:	List[Haploid]

Allele Assignment¶

class pyhml.models.allele_assignment.AlleleAssignment(allele_db: str = None, allele_version: str = None, date: str = None, glstring: List[str] = None, haploid: List[pyhml.models.haploid.Haploid] = None)[source]

Bases: pyhml.models.base_model_.Model

NOTE: This class is auto generated by the swagger code generator program. Do not edit the class manually.

allele_db

Gets the allele_db of this AlleleAssignment.

Returns:	The allele_db of this AlleleAssignment.
Return type:	str

allele_version

Gets the allele_version of this AlleleAssignment.

Returns:	The allele_version of this AlleleAssignment.
Return type:	str

date

Gets the date of this AlleleAssignment.

Returns:	The date of this AlleleAssignment.
Return type:	str

classmethod from_dict(dikt) → pyhml.models.allele_assignment.AlleleAssignment[source]

Returns the dict as a model

Parameters:	dikt – A dict.
Type:	dict
Returns:	The AlleleAssignment of this AlleleAssignment.
Return type:	AlleleAssignment

glstring

Gets the glstring of this AlleleAssignment.

Returns:	The glstring of this AlleleAssignment.
Return type:	List[str]

haploid

Gets the haploid of this AlleleAssignment.

Returns:	The haploid of this AlleleAssignment.
Return type:	List[Haploid]