Skip to content

Yilinzhao #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
yilinzhao1615 wants to merge 14 commits into
base: master
Choose a base branch
from
Open

Yilinzhao #7

Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
70562d4
modification of MERFISHProbeDesign.m by yilin
yilinzhao1615 Jan 3, 2020
bdef939
Update MERFISHProbeDesign.m
yilinzhao1615 Jan 3, 2020
a82c8fb
update allOligos
yilinzhao1615 Jan 8, 2020
9984f6b
Update MERFISHProbeDesign.m
yilinzhao1615 Jan 8, 2020
ea0b20f
Update MERFISHProbeDesign.m
yilinzhao1615 Jan 8, 2020
bc82b52
fixed bugs for genes with multiple scripts
yilinzhao1615 Jan 14, 2020
03e1e0c
Update MERFISHProbeDesign.m
yilinzhao1615 Jan 14, 2020
f07937e
Update MERFISHProbeDesign.m
yilinzhao1615 Feb 11, 2020
efa7d05
Update MERFISHProbeDesign.m
yilinzhao1615 Feb 11, 2020
3c7a065
Update MERFISHProbeDesign.m
yilinzhao1615 Feb 11, 2020
b2c08f9
remove NCBI _ to , modification
yilinzhao1615 Feb 12, 2020
efa1547
Update MERFISHProbeDesign.m
yilinzhao1615 Feb 13, 2020
84c5402
Update MERFISHProbeDesign.m
yilinzhao1615 Feb 13, 2020
8f2b238
add an output table for genes and number of probes
yilinzhao1615 Feb 13, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
76 changes: 52 additions & 24 deletions probe_construction/MERFISHProbeDesign.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -660,13 +660,15 @@ function MERFISHProbeDesign(varargin)

fprintf(logFID, '%s - Building transcriptome object.\n', datestr(datetime));

% Build transcriptome using existing abundance data
%Build transcriptome using existing abundance data
transcriptome = Transcriptome(rawTranscriptomeFasta, ...
'abundPath', fpkmPath, ...
'verbose', true, ...
'headerType', transcriptomeHeaderType, ...
'IDType', transcriptomeIDType);

%transcriptome = Transcriptome(rawTranscriptomeFasta, ...
% 'abundPath', fpkmPath, ...
% 'verbose', true);
transcriptome.Save(transcriptomePath);
fprintf(logFID, '%s - Transcriptome object saved to %s\n', datestr(datetime), transcriptomePath);

Expand Down Expand Up @@ -718,7 +720,7 @@ function MERFISHProbeDesign(varargin)
% Generate a OTTable for isoforms for the given gene
isoSpecificityTables(i) = OTTable(localTranscriptome, ...
isoSpecificityTable_lengthOfExactHomology, ... % lengthOfExactHomology is the length of exact homology used to calculate penalties
'verbose', false, ...
'verbose', false, ...
'transferAbund', false);

else
Expand Down Expand Up @@ -798,7 +800,7 @@ function MERFISHProbeDesign(varargin)
%% Create parallel pool... speeds up the construction of the TRDesigner and the construction of libraries
if isempty(gcp('nocreate'))
fprintf(logFID, '%s - Start parallel processing pool\n', datestr(datetime));
p = parpool(5); % Insert a number here appropriate to the used computational resources
p = parpool(4); % Insert a number here appropriate to the used computational resources
else
p = gcp;
end
Expand Down Expand Up @@ -915,6 +917,11 @@ function MERFISHProbeDesign(varargin)
fprintf(logFID, '%s - Target regions loaded from %s\n', datestr(datetime), trRegionsPath);
end

%write the genename
genenames={targetRegions.geneName}';
geneids={targetRegions.id}';
numRegions={targetRegions.numRegions}';
writetable(table(genenames,geneids,numRegions),[analysisSavePath 'targetRegions.csv'],'WriteRowNames',false)
%% ------------------------------------------------------------------------
% Step 2: Compile the library
% The target regions designed above will be compiled into template
Expand Down Expand Up @@ -956,13 +963,20 @@ function MERFISHProbeDesign(varargin)
% string miss-match. Replacing '_' with ',' in original codebook solves
% this issue.

if ~strcmp(transcriptomeIDType, 'NCBI')
finalIds = strrep(finalIds, '_', ',');
end
%if ~strcmp(transcriptomeIDType, 'NCBI')
% finalIds = strrep(finalIds, '_', ',');
%end

finalGenes = {codebook.name}; % Extract gene common names from codebook
barcodes = char({codebook.barcode}) == '1'; % Extract string barcodes and convert to logical matrix

%check if gene and ids match the reference
genes_from_ids=targetRegions(ismember({targetRegions.id}, finalIds));
genenames=targetRegions(ismember({targetRegions.geneName}, finalGenes));
if length(setdiff({genenames.geneName},{genes_from_ids.geneName}))>0
warning([char(setdiff({genenames.geneName},{genes_from_ids.geneName})),' ',char(setdiff({genes_from_ids.id},{genenames.id})),' is different from the reference']);
fprintf(logFID, ['WARNING! ', char(setdiff({genenames.geneName},{genes_from_ids.geneName})),' ',char(setdiff({genes_from_ids.id},{genenames.id})),' is different from the reference\n']);
end

if versionMatch
finalTargetRegions = targetRegions(ismember({targetRegions.id}, finalIds)); % Extract only the desired target regions
Expand Down Expand Up @@ -1035,13 +1049,16 @@ function MERFISHProbeDesign(varargin)
if keepGoingFlag
oligos = [];

allOligos = [];
lastGene = '';

if keepAllPossibleProbes
allHeaders = cell(sum(vertcat(finalTargetRegions.numRegions)), 1);
allSeqs = cell(sum(vertcat(finalTargetRegions.numRegions)), 1);
seqCount = 1;
end

Genes={};
ProbeNumbers={};
%if keepAllPossibleProbes
% allHeaders = cell(sum(vertcat(finalTargetRegions.numRegions)), 1);
% allSeqs = cell(sum(vertcat(finalTargetRegions.numRegions)), 1);
% seqCount = 1;
%end

for i=1:length(finalIds)
% Save local gene
Expand Down Expand Up @@ -1176,15 +1193,19 @@ function MERFISHProbeDesign(varargin)
display(['... ' headers{indsToRemove(r)}]);
end

% display(indsToKeep)

indsToKeepForReal = [indsToKeepForReal, indsToKeep];
% display(indsToKeep)

%indsToKeepForReal = [indsToKeepForReal, indsToKeep];
indsToKeepForReal = indsToKeep;
end

indsToKeepForAll = indsToKeepForReal(1:length(indsToKeepForReal));
indsToKeepForReal = indsToKeepForReal(randperm(length(indsToKeepForReal), min([length(indsToKeepForReal) numProbesPerGene])));
display(['... keeping ' num2str(length(indsToKeepForReal)) ' probes']);
fprintf(logFID, '%s - Retaining %d probes\n', datestr(datetime), length(indsToKeepForReal));
%write the genename
Genes=[Genes,localGeneName];
ProbeNumbers=[ProbeNumbers,length(indsToKeepForReal)];

% Check on number
if length(indsToKeepForReal) < numProbesPerGene
Expand Down Expand Up @@ -1253,14 +1274,18 @@ function MERFISHProbeDesign(varargin)
oligos(end+1).Header = headers{indsToKeepForReal(s)};
oligos(end).Sequence = seqs{indsToKeepForReal(s)};
end

if keepAllPossibleProbes
% Append all headers + seqs to cell
allHeaders(seqCount:(seqCount + length(headers) - 1)) = headers;
allSeqs(seqCount:(seqCount + length(seqs) - 1)) = seqs;
seqCount = seqCount + length(seqs);
for s=1:length(indsToKeepForAll)
allOligos(end+1).Header = headers{indsToKeepForAll(s)};
allOligos(end).Sequence = seqs{indsToKeepForAll(s)};
end

%if keepAllPossibleProbes
% Append all headers + seqs to cell
% allHeaders(seqCount:(seqCount + length(headers) - 1)) = headers;
% allSeqs(seqCount:(seqCount + length(seqs) - 1)) = seqs;
% seqCount = seqCount + length(seqs);
%end


else
fprintf(1, 'Empty!\n');
Expand All @@ -1281,10 +1306,13 @@ function MERFISHProbeDesign(varargin)
fastawrite(possibleOligosPath, oligos);
display(['... completed in ' num2str(toc(writeTimer))]);
fprintf(logFID, '%s - Completed in %d s\n', datestr(datetime), toc(writeTimer));

%%%%%Write out how many probes per gene as a table
Genes=Genes'
ProbeNumbers=ProbeNumbers'
writetable(table(Genes,ProbeNumbers),[analysisSavePath 'probesPerGene.csv'],'WriteRowNames',false)
if keepAllPossibleProbes

allOligos = cell2struct([allHeaders, allSeqs], {'Header', 'Sequence'}, 2);
%allOligos = cell2struct([allHeaders, allSeqs], {'Header', 'Sequence'}, 2);

PageBreak();
fprintf(1, 'Writing: %s\n', allOligosPath);
Expand Down