Cardea
cardea.fhir.
Sequence
Raw data describing a biological sequence.
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__
Initialize self. See help(type(self)) for accurate signature.
Methods
__init__([dict_values])
Initialize self.
assert_type()
assert_type
Checks class values follow set possible enumerations.
get_dataframe()
get_dataframe
Returns dataframe from class attribute values.
get_eligible_relationships()
get_eligible_relationships
Returns class relationships for attributes that are used.
get_id()
get_id
Returns fhir class identifier.
get_relationships()
get_relationships
Returns class relationships.
set_attributes(dict_values)
set_attributes
Sets values to class attributes.