9 files changed, 1240 insertions, 0 deletions
diff --git a/test/entropy/don_anal.m b/test/entropy/don_anal.m
new file mode 100644
index 0000000..7d0a648
--- a/dev/null
+++ b/test/entropy/don_anal.m
@@ -0,0 +1,40 @@
+d = fastaread('C:\dondata\FASTA2.fa');
+lens = arrayfun(@(x)(numel(x.Sequence)), d);
+d(lens < 300) = [];
+rexp = '/Human/(\w*)/([\d\w]*)/(.*?)/(\d{4})/';
+headers = cell(length(d), 1);
+[headers{:}] = deal(d(:).Header);
+groups = regexp(headers, rexp, 'tokens', 'once');
+cgroups = cat(1,groups{:});
+dates = unique(cgroups(:,end));
+
+seqs = cell(length(d), 1);
+[seqs{:}] = deal(d(:).Sequence);
+
+ALIGN_CELL = cell(length(dates), 1);
+INDS_CELL = cell(length(dates), 1);
+PAIRWISE_CELL = cell(length(dates),1);
+for i = 1:length(dates)
+    display(dates{i})
+    tf = strcmp(cgroups(:,end), dates{i});
+    if isempty(PAIRWISE_CELL{i})
+        pairwise_dists = GenomePairwiseDist(d(tf), dates{i});
+        PAIRWISE_CELL{i} = pairwise_dists;
+    else
+        pairwise_dists = PAIRWISE_CELL{i};
+    end
+    if isempty(ALIGN_CELL{i}) || isempty(INDS_CELL{i})
+        [ALIGN_CELL{i}, INDS_CELL{i}] = GenomeAlignments(d(tf), ...
+                                        pairwise_dists);
+        save restore_data PAIRWISE_CELL ALIGN_CELL INDS_CELL
+    end
+end
+
+for i = 1:length(ALIGN_CELL)
+    [ALIGN_CELL{i}, ~]= RefineAlignments(ALIGN_CELL{i});
+end
+
+
+ents = CalculateProteinEntropy(d(1), ALIGN_CELL);
+
+dents = cat(1, ents{:});