Move files

Project.toml

@@ -6,3 +6,13 @@ version = "0.1.0"
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+
+[compat]
+BioSequences = "1.1"
+julia = "1.1"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

src/BioSequenceGraphs.jl

@@ -7,12 +7,6 @@ export SequenceDistanceGraph,
 
 using BioSequences
 
-#include("Nodes.jl")
-#include("Links.jl")
-#include("SequenceGraph.jl")
-#include("IO.jl")
-include("SequenceDistanceGraph.jl")
-include("graph_building.jl")
-#include("DeBruijnGraph.jl")
-#include("GFA1/GFA1.jl")
+include("graph/SequenceDistanceGraph.jl")
+include("graph/graph_building.jl")
 end # module BioSequenceGraphs

src/graph/DistanceGraphLink.jl

@@ -0,0 +1,20 @@
+###
+### Link/Edge type for SequenceDistanceGraph
+###
+
+"""
+Represents a single distance between two sequences in a SequenceDistanceGraph.
+"""
+struct DistanceGraphLink
+    source::NodeID
+    destination::NodeID
+    dist::Int64
+end
+
+source(l::DistanceGraphLink) = l.source
+destination(l::DistanceGraphLink) = l.destination
+distance(l::DistanceGraphLink) = l.dist
+
+"Test if link `l` is a forward link leaving node `n`."
+is_forwards_from(l::DistanceGraphLink, n::NodeID) = source(l) == -n
+is_backwards_from(l::DistanceGraphLink, n::NodeID) = source(l) == n

src/graph/SDGNode.jl

@@ -0,0 +1,55 @@
+###
+### Node type for SequenceDistanceGraph
+###
+
+"""
+The SDGNode type represents a node in a SequenceDistanceGraph.
+
+At present it contains only two fields, first it holds an instance of a BioSequences
+Sequence type.
+
+Secondly, it tracks a flag which indicates if the node has been
+deleted or not.
+
+!!! note
+    The deleted flag allows us to mark nodes in the graph as deleted, which can be of
+    help in some algorithms where the graph structure is being edited (merging nodes for example).
+
+    Actually deleting the node would shift node IDs and require redoing all links in the graph
+    and so on.
+
+    So just marking a node as deleted and not using it anymore is a lazy but sometimes
+    helpful choice.
+"""
+struct SDGNode{S}
+    seq::S
+    deleted::Bool
+end
+
+function empty_node(::Type{S}) where {S <: Sequence}
+    return SDGNode{S}(empty_seq(S), true)
+end
+
+# TODO: This is a hacked copy of the dna string literal macro from BioSequences,
+# except it creates 2-bit based DNA sequences rather than 4 bit based ones.
+# This ability to choose the bit encoding should make its way to BioSequences.jl
+# in the future, but for now, it's here.
+#
+# I basically want this as it lets me create a single literal empty sequence, shared
+# by all deleted SDG nodes. Rather than having each deleted SDG node create a new empty
+# sequence.
+macro dna2_str(seq, flag)
+    if flag == "s"
+        return BioSequence{DNAAlphabet{2}}(BioSequences.remove_newlines(seq))
+    elseif flag == "d"
+        return quote
+            BioSequence{DNAAlphabet{2}}($(BioSequences.remove_newlines(seq)))
+        end
+    end
+    error("Invalid DNA flag: '$(flag)'")
+end
+
+@inline empty_seq(::Type{BioSequence{DNAAlphabet{2}}}) = dna2""s
+
+@inline is_deleted(n::SDGNode{S}) where {S<:Sequence} = n.deleted
+@inline length(n::SDGNode{S}) where {S<:Sequence} = length(n.seq)

src/SequenceDistanceGraph.jl → src/graph/SequenceDistanceGraph.jl

@@ -1,74 +1,17 @@
-
-# Node and Link types for SequenceDistanceGraph
-# ---------------------------------------------
+###
+### Node and Link types for SequenceDistanceGraph
+###
 
 const NodeID = Int64
 
-"""
-The SDGNode type represents a node in a SequenceDistanceGraph.
-
-At present it contains only two fields, first it holds an instance of a BioSequences
-Sequence type.
-
-Secondly, it tracks a flag which indicates if the node has been
-deleted or not.
-
-!!! note
-    The deleted flag allows us to mark nodes in the graph as deleted, which can be of
-    help in some algorithms where the graph structure is being edited (merging nodes for example).
-
-    Actually deleting the node would shift node IDs and require redoing all links in the graph
-    and so on.
-
-    So just marking a node as deleted and not using it anymore is a lazy but sometimes
-    helpful choice.
-"""
-struct SDGNode{S}
-    seq::S
-    deleted::Bool
-end
-
-function empty_node(::Type{S}) where {S <: Sequence}
-    return SDGNode{S}(empty_seq(S), true)
-end
-
-# TODO: This is a hacked copy of the dna string literal macro from BioSequences,
-# except it creates 2-bit based DNA sequences rather than 4 bit based ones.
-# This ability to choose the bit encoding should make its way to BioSequences.jl
-# in the future, but for now, it's here.
-#
-# I basically want this as it lets me create a single literal empty sequence, shared
-# by all deleted SDG nodes. Rather than having each deleted SDG node create a new empty
-# sequence.
-macro dna2_str(seq, flag)
-    if flag == "s"
-        return BioSequence{DNAAlphabet{2}}(BioSequences.remove_newlines(seq))
-    elseif flag == "d"
-        return quote
-            BioSequence{DNAAlphabet{2}}($(BioSequences.remove_newlines(seq)))
-        end
-    end
-    error("Invalid DNA flag: '$(flag)'")
-end
-
-empty_seq(::Type{BioSequence{DNAAlphabet{2}}}) = dna2""s
-
-"""
-Represents a single distance between two sequences in a SequenceDistanceGraph.
-"""
-struct DistanceGraphLink
-    source::NodeID
-    destination::NodeID
-    dist::Int64
-end
+include("SDGNode.jl")
+include("DistanceGraphLink.jl")
 
-source(l::DistanceGraphLink) = l.source
-destination(l::DistanceGraphLink) = l.destination
-distance(l::DistanceGraphLink) = l.dist
+const LinksT = Vector{Vector{DistanceGraphLink}}
 
-"Test if link `l` is a forward link leaving node `n`."
-is_forwards_from(l::DistanceGraphLink, n::NodeID) = source(l) == -n
-is_backwards_from(l::DistanceGraphLink, n::NodeID) = source(l) == n
+###
+### Graph types
+###
 
 """
 The SequenceDistanceGraph is a representation of a genome assembly.
@@ -105,6 +48,7 @@ function SequenceDistanceGraph{S}() where {S<:Sequence}
 end
 
 n_nodes(sg::SequenceDistanceGraph) = length(nodes(sg))
+each_node_id(sg::SequenceDistanceGraph) = eachindex(nodes(sg))
 
 # Graph accessor functions
 # ------------------------
@@ -113,8 +57,6 @@ nodes(sg::SequenceDistanceGraph) = sg.nodes
 node(sg::SequenceDistanceGraph, i::NodeID) = nodes(sg)[abs(i)]
 links(sg::SequenceDistanceGraph) = sg.links
 
-
-
 """
     links(sg::SequenceGraph, node::NodeID)
 
@@ -290,17 +232,6 @@ function get_previous_nodes(sg::SequenceDistanceGraph, n::NodeID)
     end
 end
 
-#=
-function find_tips(sg::SequenceDistanceGraph)
-    r = Vector{NodeID}()
-    for l in links(sg)
-        if length(l) == 1
-            d = destination(l[1])
-            for ol in links(sg, d)
-                
-end
-=#
-
 function dump_to_gfa1(sg, filename)
     fasta_filename = "$filename.fasta"
     gfa = open("$filename.gfa", "w")
@@ -337,5 +268,3 @@ function dump_to_gfa1(sg, filename)
     close(gfa)
     close(fasta)
 end
-
-

src/graph_building.jl → src/graph/graph_building.jl

@@ -240,3 +240,5 @@ function new_graph_from_kmerlist(kmerlist::Vector{DNAKmer{K}}) where {K}
     @info string("Done c", str)
     return sg
 end
+SequenceDistanceGraph(kmerlist::Vector{DNAKmer{K}}) where {K} = new_graph_from_kmerlist(kmerlist)
+

test/runtests.jl

@@ -1,5 +1,5 @@
 using BioSequenceGraphs
-using Base.Test
+using Test
 
 # write your own tests here
 @test 1 == 1