spark_auto_mapper_fhir.resources.molecular_sequence

Module Contents

Classes

MolecularSequence

MolecularSequence
class spark_auto_mapper_fhir.resources.molecular_sequence.MolecularSequence(*, id_=None, meta=None, implicitRules=None, language=None, text=None, contained=None, extension=None, modifierExtension=None, identifier=None, type_=None, coordinateSystem, patient=None, specimen=None, device=None, performer=None, quantity=None, referenceSeq=None, variant=None, observedSeq=None, quality=None, readCoverage=None, repository=None, pointer=None, structureVariant=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_resource_base.FhirResourceBase

MolecularSequence molecularsequence.xsd

Raw data describing a biological sequence. If the element is present, it must have either a @value, an @id, or extensions

Raw data describing a biological sequence. If the element is present, it must have either a @value, an @id, or extensions

param id_

The logical id of the resource, as used in the URL for the resource. Once

assigned, this value never changes.
param meta

The metadata about the resource. This is content that is maintained by the

infrastructure. Changes to the content might not always be associated with version changes to the resource.

param implicitRules

A reference to a set of rules that were followed when the resource was

constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.

param language

The base language in which the resource is written.

param text

A human-readable narrative that contains a summary of the resource and can be

used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it “clinically safe” for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.

param contained

These resources do not have an independent existence apart from the resource

that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

param extension

May be used to represent additional information that is not part of the basic

definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

param modifierExtension

May be used to represent additional information that is not part of the basic

definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element’s descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

param identifier

A unique identifier for this particular sequence instance. This is a FHIR-

defined id.
param type_

Amino Acid Sequence/ DNA Sequence / RNA Sequence.

param coordinateSystem

Whether the sequence is numbered starting at 0 (0-based numbering or

coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).

param patient

The patient whose sequencing results are described by this resource.

param specimen

Specimen used for sequencing.

param device

The method for sequencing, for example, chip information.

param performer

The organization or lab that should be responsible for this result.

param quantity

The number of copies of the sequence of interest. (RNASeq).

param referenceSeq

A sequence that is used as a reference to describe variants that are present

in a sequence analyzed.
param variant

The definition of variant here originates from Sequence ontology ([variant_of]

(http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

param observedSeq

Sequence that was observed. It is the result marked by referenceSeq along with

variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.

param quality

An experimental feature attribute that defines the quality of the feature in a

quantitative way, such as a phred quality score ([SO:0001686](http://www.seque nceontology.org/browser/current_svn/term/SO:0001686)).

param readCoverage

Coverage (read depth or depth) is the average number of reads representing a

given nucleotide in the reconstructed sequence.
param repository

Configurations of the external repository. The repository shall store target’s

observedSeq or records related with target’s observedSeq.
param pointer

Pointer to next atomic sequence which at most contains one variant.

param structureVariant

Information about chromosome structure variation.

Parameters
get_schema(self, include_extension)
Parameters

include_extension (bool) –

Return type

Optional[Union[pyspark.sql.types.StructType, pyspark.sql.types.DataType]]