finished basic modeller examples adaption for julia

src/MODELLER/modeller-basic-example-julia/plot_profiles.jl

@@ -0,0 +1,58 @@
+using PyCall
+using PyPlot
+
+@pyimport modeller
+@pyimport pylab
+
+function r_enumerate(seq)
+    """Enumerate a sequence in reverse order"""
+    # Note that we don"t use reversed() since Python 2.3 doesn"t have it
+    num = pybuiltin(:len)(seq) - 1
+    while num >= 0
+        produce((num, get(seq, num)))
+        num -= 1
+    end
+end
+
+function get_profile(profile_file, seq)
+    """Read `profile_file` into a Python array, and add gaps corresponding to
+       the alignment sequence `seq`."""
+    # Read all non-comment and non-blank lines from the file:
+    f = open(profile_file)
+    vals = Any[]
+    for line in eachline(f)
+        if line[1] != '#' && length(line) > 10
+            spl = split(line)
+            push!(vals, float(last(spl)))
+        end
+    end
+    close(f)
+    # Insert gaps into the profile corresponding to those in seq:
+    taskAtr = @task r_enumerate(seq[:residues])
+    for x in taskAtr
+        n = x[1]
+        res = x[2]
+        for gap in range(1, res[:get_leading_gaps]())
+            # Julia arrays start from 1 so we have to add 1 to the position
+            insert!(vals, n+1, nothing)
+        end
+    end
+    # Add a gap at position "0", so that we effectively count from 1:
+    insert!(vals, 1, nothing)
+    return vals
+end
+
+e = modeller.environ()
+a = modeller.alignment(e, file="TvLDH-1bdmA.ali")
+
+template = get_profile("1bdmA.profile", get(a, "1bdmA"))
+model = get_profile("TvLDH.profile", get(a, "TvLDH"))
+
+# Plot the template and model profiles in the same plot for comparison:
+figure(1, figsize=(10,6))
+xlabel("Alignment position")
+ylabel("DOPE per-residue score")
+plot(model, color="red", linewidth=2, label="Model")
+plot(template, color="green", linewidth=2, label="Template")
+legend()
+savefig("dope_profile.png", dpi=65)