cardea.fhir.Sequence

class cardea.fhir.Sequence(dict_values=None)

Raw data describing a biological sequence.

Parameters

  • resourceType – This is a Sequence resource

  • identifier – A unique identifier for this particular sequence instance. This is a FHIR-defined id.

  • type – Amino Acid Sequence/ DNA Sequence / RNA Sequence.

  • 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).

  • patient – The patient whose sequencing results are described by this resource.

  • specimen – Specimen used for sequencing.

  • device – The method for sequencing, for example, chip information.

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

  • quantity – The number of copies of the seqeunce of interest. (RNASeq).

  • referenceSeq – A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

  • 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.

  • observedSeq – Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd.

  • 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.sequenceontology.org/browser/current_svn/term/SO:0001686)).

  • readCoverage – Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

  • repository – Configurations of the external repository. The repository shall store target’s observedSeq or records related with target’s observedSeq.

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

__init__(dict_values=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__([dict_values])

Initialize self.

assert_type()

Checks class values follow set possible enumerations.

get_dataframe()

Returns dataframe from class attribute values.

get_eligible_relationships()

Returns class relationships for attributes that are used.

get_id()

Returns fhir class identifier.

get_relationships()

Returns class relationships.

set_attributes(dict_values)

Sets values to class attributes.
cardea.fhir.SearchParameter cardea.fhir.ServiceDefinition