Merge pull request #625 from diegozea/master

Use MIToS v3

Project.toml

@@ -57,8 +57,8 @@ ImageCore = "0.9, 0.10"
 ImageShow = "0.3"
 JSON3 = "1"
 Lazy = "0.15"
-MIToS = "2"
-Makie = "0.21"
+MIToS = "3"
+Makie = "0.19, 0.20, 0.21"
 Meshes = "0.46"
 MolecularGraph = "0.13, 0.14, 0.15, 0.16"
 OrderedCollections = "1.4"

README.md

@@ -51,9 +51,8 @@ reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")
 msa = [reader...] |> Observable
 close(reader)
 ## or 
-using MIToS
 using MIToS.MSA
-msa = MIToS.MSA.read("pf00062.stockholm.gz", Stockholm)
+msa = read_file("pf00062.stockholm.gz", Stockholm)
 
 fig = plotmsa(msa; colorscheme = :tableau_blue_green)
 ```

docs/src/index.md

@@ -80,9 +80,8 @@ reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")
 msa = [reader...] |> Observable
 close(reader)
 ## or 
-using MIToS
 using MIToS.MSA
-msa = MIToS.MSA.read("pf00062.stockholm.gz", Stockholm)
+msa = read_file("pf00062.stockholm.gz", Stockholm)
 
 fig = plotmsa(msa; colorscheme = :tableau_blue_green)
 ```

docs/src/msaselection.md

@@ -10,12 +10,11 @@ are plotted on the right.
 ## Copy-pastable code
 ````julia
 using BioMakie
-using MIToS
 using MIToS.MSA, MIToS.Pfam
 using GLMakie
 using Lazy
 downloadpfam("pf00062")
-msa1 = MIToS.MSA.read("pf00062.stockholm.gz",Stockholm)
+msa1 = read_file("pf00062.stockholm.gz",Stockholm)
 msa2 = Observable(msa1)
 plotdata = plottingdata(msa2)
 fig = Figure(resolution = (1400,400))
@@ -61,7 +60,6 @@ xlims!(ax, (0, 23))
 ## Imports
 ````julia
 using BioMakie
-using MIToS
 using MIToS.MSA, MIToS.Pfam
 using GLMakie
 using Lazy
@@ -72,7 +70,7 @@ Use MIToS to download a Pfam MSA, then prepare the plotting data.
 
 ````julia
 downloadpfam("pf00062")
-msa1 = MIToS.MSA.read("pf00062.stockholm.gz",Stockholm)
+msa1 = read_file("pf00062.stockholm.gz",Stockholm)
 msa2 = Observable(msa1)
 plotdata = plottingdata(msa2)
 ````

src/msa.jl

@@ -666,8 +666,8 @@ a Figure and Observables for interaction.
 # Examples
 ```julia
 MIToS.Pfam.downloadpfam("PF00062")	# download PF00062 MSA
-msa = MIToS.MSA.read("PF00062.stockholm.gz", Stockholm, 
-					generatemapping =true, useidcoordinates=true)
+msa = MIToS.MSA.read_file("PF00062.stockholm.gz", Stockholm, 
+	generatemapping =true, useidcoordinates=true)
 
 plotmsa( msa; kwargs... )
 ```

src/otherplots.jl

@@ -16,8 +16,8 @@ Plot a MIToS distance or contact map.
 using MIToS.PDB
 
 pdbfile = MIToS.PDB.downloadpdb("1IVO", format=PDBFile)
-residues_1ivo = read(pdbfile, PDBFile)
-pdb = @residues residues_1ivo model "1" chain "A" group "ATOM" residue All
+residues_1ivo = read_file(pdbfile, PDBFile)
+pdb = select_residues(residues_1ivo, model="1", chain="A", group="ATOM")
 dmap = MIToS.PDB.distance(pdb, criteria="All") # distance map
 cmap = contact(pdb, 8.0, criteria="CB") # contact map
 
@@ -66,8 +66,8 @@ fig = Figure()
 using MIToS.PDB
 
 pdbfile = MIToS.PDB.downloadpdb("1IVO", format=PDBFile)
-residues_1ivo = read(pdbfile, PDBFile)
-pdb = @residues residues_1ivo model "1" chain "A" group "ATOM" residue All
+residues_1ivo = read_file(pdbfile, PDBFile)
+pdb = select_residues(residues_1ivo, model="1", chain="A", group="ATOM")
 dmap = MIToS.PDB.distance(pdb, criteria="All") # distance map 
 cmap = contact(pdb, 8.0, criteria="CB") # contact map
 

src/structure.jl

@@ -506,14 +506,14 @@ fig = Figure()
 
 using MIToS.PDB
 
-pdbfile = MIToS.PDB.downloadpdb("2vb1")
-struc = MIToS.PDB.read(pdbfile, PDBML) |> Observable
+pdbfile = MIToS.PDB.downloadpdb("2vb1", format=PDBFile)
+struc = MIToS.PDB.read_file(pdbfile, PDBFile) |> Observable
 strucplot = plotstruc!(fig, struc)
 
-chain_A = @residues struc model "1" chain "A" group "ATOM" residue All
+chain_A = select_residues(struc, model="1", chain="A", group="ATOM")
 strucplot = plotstruc!(fig, chain_A)
 
-chnatms = @atoms struc model "1" chain "A" group "ATOM" residue All atom All
+chnatms = select_atoms(struc, model="1", chain="A", group="ATOM")
 strucplot = plotstruc!(fig, chnatms)
 -------------------------
 using BioStructures
@@ -1135,14 +1135,14 @@ Create and return a Makie Figure for a protein structural element.
 ```julia
 using MIToS.PDB
 
-pdbfile = MIToS.PDB.downloadpdb("2vb1")
-struc = MIToS.PDB.read(pdbfile, PDBML) |> Observable
+pdbfile = MIToS.PDB.downloadpdb("2vb1", format=PDBFile)
+struc = MIToS.PDB.read_file(pdbfile, PDBFile) |> Observable
 strucplot = plotstruc(struc)
 
-chain_A = @residues struc model "1" chain "A" group "ATOM" residue All
+chain_A = select_residues(struc, model="1", chain="A", group="ATOM")
 strucplot = plotstruc(chain_A)
 
-chnatms = @atoms struc model "1" chain "A" group "ATOM" residue All atom All
+chnatms = select_atoms(struc, model="1", chain="A", group="ATOM")
 strucplot = plotstruc(chnatms)
 -------------------------
 using BioStructures

test/runtests.jl

@@ -168,9 +168,9 @@ firstvalue(dict::AbstractDict) = first(values(dict))
     @test atmcolors[][end] == RGB{Float64}(0.65,0.96,0.7)
 
     # MIToS
-    struc = MIToS.PDB.read("$(dir)/2VB1.pdb", MIToS.PDB.PDBFile);
-    chn = MIToS.PDB.@residues struc model "1" chain "A" group "ATOM" residue All
-    atms = MIToS.PDB.@atoms chn model "1" chain "A" group "ATOM" residue All atom All
+    struc = MIToS.PDB.read_file("$(dir)/2VB1.pdb", MIToS.PDB.PDBFile);
+    chn = MIToS.PDB.select_residues(struc, model="1", chain="A", group="ATOM")
+    atms = MIToS.PDB.select_atoms(chn, model="1", chain="A", group="ATOM")
     struc_obs = Observable(struc);
     chn_obs = Observable(chn);
     atms_obs = Observable(atms);
@@ -252,7 +252,7 @@ end
 @testset "MSA plotting" begin
     # MIToS
     downloadpfam("pf00062")
-    msa1 = MIToS.MSA.read("pf00062.stockholm.gz",Stockholm)
+    msa1 = MIToS.MSA.read_file("pf00062.stockholm.gz",Stockholm)
     @test size(msa1) == (3023, 123)
     @test length(msa1.annotations.sequences) == 3023
     plotdata = plottingdata(msa1)