Get tests passing

Now that alignments are back on Interpro, we can fix errors in the new
implementions.

src/alphafold.jl

@@ -11,7 +11,7 @@ alphafoldfilename(uniprotXname; version=4) = "AF-$uniprotXname-F1-model_v$versio
 Return the latest version of the AlphaFold file for `uniprotXname` in `dirname`.
 If `join` is `true`, then the full path is returned.
 """
-function alphafoldfile(uniprotXname, dirname=pwd(); join::Bool=false)
+function alphafoldfile(uniprotXname::AbstractString, dirname=pwd(); join::Bool=false)
     rex = regex_alphafold_pdb(uniprotXname)
     lv = 0
     for fn in readdir(dirname)
@@ -52,7 +52,7 @@ end
 
 Return a dictionary mapping `MSACode`s to the corresponding AlphaFold structure files.
 """
-function alphafoldfiles(msa::AnnotatedMultipleSequenceAlignment, dirname=pwd())
+function alphafoldfiles(msa::AnnotatedMultipleSequenceAlignment, dirname=pwd(); join::Bool=false)
     afs = alphafoldfiles(dirname)
     accesscode2idx = Dict{AccessionCode,Int}()
     for (i, af) in pairs(afs)
@@ -63,7 +63,8 @@ function alphafoldfiles(msa::AnnotatedMultipleSequenceAlignment, dirname=pwd())
     for name in sequencenames(msa)
         ac = AccessionCode(msa, name)
         if haskey(accesscode2idx, ac)
-            msacode2structfile[MSACode(name)] = afs[accesscode2idx[ac]]
+            fn = afs[accesscode2idx[ac]]
+            msacode2structfile[MSACode(name)] = join ? joinpath(dirname, fn) : fn
         end
     end
     return msacode2structfile

src/chimerax.jl

@@ -22,7 +22,7 @@ function chimerax_script(scriptfilename, struct_filenames, ridxs::AbstractVector
             end
         end
         if isa(extras, AbstractString)
-            println(io, extras) 
+            println(io, extras)
         else
             for ex in extras
                 println(io, ex)
@@ -68,12 +68,12 @@ function chimerax_script(scriptfilename, uprot_list, msa::AnnotatedMultipleSeque
     ridxs = [Int[] for _ in 1:length(uprot_list)]
     struct_filenames = Vector{String}(undef, length(uprot_list))
     rcstyles = Dict{Tuple{Int,Int},String}()
-    afs = alphafoldfile(msa, dir; join=true)
+    afs = alphafoldfiles(msa, dir; join=true)
     uprot2msaidx = Dict{AccessionCode,Int}(AccessionCode(msa, name) => i for (i, name) in enumerate(sequencenames(msa)))
     for (i, p) in enumerate(uprot_list)
         j = uprot2msaidx[AccessionCode(p)]
-        struct_filenames[i] = afs[MSACode(sequencenames(msa, j))]
-        sm = getsequencemapping(msa, seqidx)
+        struct_filenames[i] = afs[MSACode(sequencenames(msa)[j])]
+        sm = getsequencemapping(msa, j)
         for (j, c) in enumerate(colidxs)
             ridx = sm[c]
             if iszero(ridx)

test/runtests.jl

@@ -285,7 +285,7 @@ using Test
                 msacode2structfile = alphafoldfiles(msa, path)
                 afnbyidx(i) = getchain(joinpath(path, msacode2structfile[MSACode(sequencenames(msa)[i])]))
 
-                c1, c2 = getchain(afnbyidx(1)), getchain(afnbyidx(5))
+                c1, c2 = afnbyidx(1), afnbyidx(5)
                 conserved_residues = c1[SequenceMapping(getsequencemapping(msa, 1))[conserved_cols]]
                 badidx = findall(==(nothing), conserved_residues)
                 conserved_residues = convert(Vector{PDBResidue}, conserved_residues[Not(badidx)])
@@ -305,7 +305,7 @@ using Test
                 # Choose a sufficiently-divergent pair that structural alignment is nontrivial
                 idxref = findfirst(str -> startswith(str, "K7N701"), sequencenames(msa))
                 idxcmp = findfirst(str -> startswith(str, "K7N778"), sequencenames(msa))
-                cref, ccmp = getchain(afnbyidx(idxref)), getchain(afnbyidx(idxcmp))
+                cref, ccmp = afnbyidx(idxref), afnbyidx(idxcmp)
                 sa = StructAlign(cref, ccmp, joinpath(@__DIR__, "tmalign.txt"))
                 @test !ismapped(sa, 1, nothing)
                 @test  ismapped(sa, 11, nothing)
@@ -335,11 +335,11 @@ using Test
                 @test length(setdiff(idxclose, sa.m2.a2s)) < 0.05 * length(idxclose)  # almost same as TMalign
 
                 chimerafile = tempname() * ".cxc"
-                chimerax_script(chimerafile, ["K7N775", "K7N731"], msa, [66, 69]; dir="somedir")
+                chimerax_script(chimerafile, ["K7N775", "K7N731"], msa, [66, 69]; dir=path)
                 script = read(chimerafile, String)
-                @test  occursin("open somedir/AF-K7N775", script)
-                @test  occursin("open somedir/AF-K7N731", script)
-                @test !occursin("open somedir/AF-K7N701", script)
+                @test  occursin("open $path/AF-K7N775", script)
+                @test  occursin("open $path/AF-K7N731", script)
+                @test !occursin("open $path/AF-K7N701", script)
                 @test occursin("show #1 :67", script)
                 @test occursin("show #1 :70", script)
                 @test occursin("show #2 :70", script)