:py:mod:`spark_auto_mapper_fhir.resources.molecular_sequence` ============================================================= .. py:module:: spark_auto_mapper_fhir.resources.molecular_sequence Module Contents --------------- Classes ~~~~~~~ .. autoapisummary:: spark_auto_mapper_fhir.resources.molecular_sequence.MolecularSequence .. py:class:: 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: :py:obj:`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. .. py:method:: get_schema(self, include_extension)