spark_auto_mapper_fhir.backbone_elements.molecular_sequence_variant

Module Contents

Classes

MolecularSequenceVariant

MolecularSequence.Variant
class spark_auto_mapper_fhir.backbone_elements.molecular_sequence_variant.MolecularSequenceVariant(*, id_=None, extension=None, modifierExtension=None, start=None, end=None, observedAllele=None, referenceAllele=None, cigar=None, variantPointer=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_backbone_element_base.FhirBackboneElementBase

MolecularSequence.Variant

Raw data describing a biological sequence.

Raw data describing a biological sequence.

param id_

None

param extension

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

definition of the element. 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 element and that modifies the understanding of the element in which it is contained 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 can 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 start

Start position of the variant on the reference sequence. If the coordinate

system is either 0-based or 1-based, then start position is inclusive.
param end

End position of the variant on the reference sequence. If the coordinate

system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.

param observedAllele

An allele is one of a set of coexisting sequence variants of a gene ([SO:00010

23](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

param referenceAllele

An allele is one of a set of coexisting sequence variants of a gene ([SO:00010

23](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end.

param cigar

Extended CIGAR string for aligning the sequence with reference bases. See

detailed documentation [here](http://support.illumina.com/help/SequencingAnaly sisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_Ext endedCIGARFormat.htm).

param variantPointer

A pointer to an Observation containing variant information.

Parameters