Representing genomci loci

The easiest way to create a locus is to use the constructor Locus(s), which takes an AbstractString s and parses it as a GenBank locus string as defined here: https://www.insdc.org/submitting-standards/feature-table/#3.4. Note that remote entry descriptors have not been implemented.

Internal representation

Since v0.4.0, genomic loci are represented using instances of AbstractLocus. Simple descriptors are represented with PointLocus{T} and SpanLocus{T}, where T is an AbstractDescriptor:

GenBank string	GenomicAnnotations representation	Description
1	`PointLocus{SingleNucleotide}(1)`	Refers to a single nucleotide.
1^2	`PointLocus{BetweenNucleotides}(1)`	Refers to the internucleotide space immediately after position 1.
10..20	`SpanLocus{ClosedSpan}(10:20)`	Denotes a closed sequence span.
10..>20	`SpanLocus{OpenRightSpan}(10:20)`	Denotes a sequence span where the right side is open, i.e. the end-point is undefined but earliest at position 20.
<10..20	`SpanLocus{OpenLeftSpan}(10:20)`	The left end-point is undefined.
<10..>20	`SpanLocus{OpenSpan}(10:20)`	Both end-points are undefined.

These can be wrapped in Complement for loci on the complement strand, e.g. Complement(SpanLocus{ClosedSpan}(10:20)) representing "complement(10..20)". Simplified constructors are provided for all AbstractDescriptors, e.g. ClosedSpan(1:10) == SpanLocus(1:10, ClosedSpan).

Compound loci are represented with Join and Order. Both types have a single field, loc which contains any number of simple descriptors. They can be wrapped with complement, as can the individual elements in loc.

Locus("complement(join(10..20,30..>40))") isa Complement{Join{SpanLocus{ClosedSpan}, SpanLocus{OpenRightSpan}}}

Iteration

AbstractLocus instances are themselves iterable, yielding each compound locus in sequence. If the locus is wrapped in Complement, the compound loci are returned in reverse order, and individually wrapped in Complement.

julia> for loc in Locus("complement(join(1..3,7..9))")
           println(loc)
       end
complement(7..9)
complement(1..3)

The eachposition(locus) function is provided for iterating over the individual genomic positions in the locus. Note that this ignores any metadata such as strandedness.

julia> for p in eachposition(Locus("complement(join(1..3,7..9))"))
           print(p)
       end
987321