spark_auto_mapper_fhir.backbone_elements.molecular_sequence_quality

Module Contents

Classes

MolecularSequenceQuality

MolecularSequence.Quality
class spark_auto_mapper_fhir.backbone_elements.molecular_sequence_quality.MolecularSequenceQuality(*, id_=None, extension=None, modifierExtension=None, type_, standardSequence=None, start=None, end=None, score=None, method=None, truthTP=None, queryTP=None, truthFN=None, queryFP=None, gtFP=None, precision=None, recall=None, fScore=None, roc=None)

Bases: spark_auto_mapper_fhir.base_types.fhir_backbone_element_base.FhirBackboneElementBase

MolecularSequence.Quality

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 type_

INDEL / SNP / Undefined variant.

param standardSequence

Gold standard sequence used for comparing against.

param start

Start position of the sequence. If the coordinate system is either 0-based or

1-based, then start position is inclusive.
param end

End position of the 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 score

The score of an experimentally derived feature such as a p-value ([SO:0001685]

(http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
param method

Which method is used to get sequence quality.

param truthTP

True positives, from the perspective of the truth data, i.e. the number of

sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

param queryTP

True positives, from the perspective of the query data, i.e. the number of

sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.

param truthFN

False negatives, i.e. the number of sites in the Truth Call Set for which

there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.

param queryFP

False positives, i.e. the number of sites in the Query Call Set for which

there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.

param gtFP

The number of false positives where the non-REF alleles in the Truth and Query

Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).

param precision

QUERY.TP / (QUERY.TP + QUERY.FP).

param recall

TRUTH.TP / (TRUTH.TP + TRUTH.FN).

param fScore

Harmonic mean of Recall and Precision, computed as: 2 * precision * recall /

(precision + recall).
param roc

Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity

tradeoff.

Parameters