AIBS version merge - bug fixes, clarification, feature adds, and refactor to object-oriented execution

.gitignore

@@ -1,17 +1,8 @@
-#################
-## Matlab
-#################
-*.asv
-*.m~
-
-#################
-## export_fig
-#################
-.ignore/
-
-#################
-## Example MERFISH data
-#################
-MERFISH_Examples/
-MERFISH_Examples2/
-
+# ignore all files...
+*.*
+# except
+!*.m
+!./README.md
+!/MERFISH_Examples2/codebookMusmusculusHypothalamus_v01.csv
+!/MERFISH_Examples2/readoutsHypothalamus.fasta
+!/MERFISH_Examples2/Mus_musculus_proxy.fpkm_tracking

AIBSProbeDesign/probeEquivalenceChecks.m

@@ -0,0 +1,86 @@
+check = zeros(length(NicovichfinalTargetRegions), 1, 'int8');
+for k = 1:length(check)
+    if fTR(k).numRegions > 0
+        check(k) = int8(strcmp(MoffittfinalTargetRegions(k).sequence{1}, NicovichfinalTargetRegions(k).sequence{1}));
+    else
+        check(k) = -1;
+    end
+end
+
+
+%%
+check = zeros(length(fTR), 4, 'int8');
+for k = 1:size(check, 1)
+
+    % Newest headers are equivalent between JM, PRN code
+    mPOHeader = strsplit(moffittPossibleOligos_again.headers{k}, ' ');
+    mLong = cell2mat(cellfun(@length, mPOHeader, 'UniformOutput', false));
+    mwhichLong = find(mLong == max(mLong(:)));
+    tPOHeader = strsplit(testPossibleOligos_again.headers{k}, ' ');
+    tLong = cell2mat(cellfun(@length, tPOHeader, 'UniformOutput', false));
+    twhichLong = find(tLong == max(tLong(:)));
+
+    check(k, 1) = int8(strcmp(mPOHeader{mwhichLong}, tPOHeader{twhichLong}));
+
+    % Headers are equivalent between consecutive runs of JM code
+    mPOHeader = strsplit(moffittPossibleOligos.headers{k}, ' ');
+    mLong = cell2mat(cellfun(@length, mPOHeader, 'UniformOutput', false));
+    mwhichLong = find(mLong == max(mLong(:)));
+    tPOHeader = strsplit(moffittPossibleOligos_again.headers{k}, ' ');
+    tLong = cell2mat(cellfun(@length, tPOHeader, 'UniformOutput', false));
+    twhichLong = find(tLong == max(tLong(:)));
+
+    check(k, 2) = int8(strcmp(mPOHeader{mwhichLong}, tPOHeader{twhichLong}));
+
+    % Headers are equivalent between consecutive runs of PRN code
+    mPOSeq = strsplit(testPossibleOligos.seqs{k}, ' ');
+    mLong = cell2mat(cellfun(@length, mPOSeq, 'UniformOutput', false));
+    mwhichLong = find(mLong == max(mLong(:)));
+    tPOSeq = strsplit(testPossibleOligos_again.seqs{k}, ' ');
+    tLong = cell2mat(cellfun(@length, tPOSeq, 'UniformOutput', false));
+    twhichLong = find(tLong == max(tLong(:)));
+
+    check(k, 3) = int8(strcmp(mPOSeq{mwhichLong}, tPOSeq{twhichLong}));
+
+    % Newest sequences are equivalent between JM, PRN code
+    mPOSeq = strsplit(moffittPossibleOligos_again.seqs{k}, ' ');
+    mLong = cell2mat(cellfun(@length, mPOSeq, 'UniformOutput', false));
+    mwhichLong = find(mLong == max(mLong(:)));
+    tPOSeq = strsplit(testPossibleOligos_again.seqs{k}, ' ');
+    tLong = cell2mat(cellfun(@length, tPOSeq, 'UniformOutput', false));
+    twhichLong = find(tLong == max(tLong(:)));
+
+    check(k, 4) = int8(strcmp(mPOSeq{mwhichLong}, tPOSeq{twhichLong}));
+end
+
+%%
+i = 140;
+localGeneName = 'NHSL2';
+all(tRegionPull.startPos == tRegionPull_Nicovich.startPos)
+all(tRegionPull.startPos == tRegionPull_Moffitt.startPos)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+

MERFISH_Examples2/codebookMusmusculusHypothalamus_v01.csv

@@ -0,0 +1,216 @@
+version, 1.0
+codebook_name, AIBS_Musmusculus_HY
+bit_names, RS0015, RS0083, RS0095, RS0109, RS0175, RS0237, RS0247, RS0255, RS0307, RS0332, RS0343, RS0384, RS0406, RS0451, RS0468, RS0548, RS0578, RS0584, RS0639, RS0707, RS0708, RS0730, RS0793, RS0805, RS0820, RS0896, RS0994, RS1047, RS3505, RS3544, RS3583, RS3592, RS3602, RS3791, RS3811, RS1520,RS1199
+name, id, barcode
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+Amigo2, uc011zyl.1, 0000000001010110000000000000000000000
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MERFISH_Examples2/libraryDesign/checkIsoformsAbundance.m

@@ -0,0 +1,9 @@
+
+
+tt = strfind({targetRegions.geneName}, 'UBC');
+ff = [];
+for k = 1:length(tt)
+    if ~isempty(tt{k})
+        ff = [ff; k];
+    end
+end