Add FilterStructArray.m

2_GeneralScripts/FilterStructArray_by_PH.m

@@ -0,0 +1,97 @@
+%
+%
+%%%%%%%%%%%%%%%%   FilterStructArray created by Philipp  %%%%%%%%%%%%%%%%%%%%%%%%
+%
+%
+% What this script does: It loads a struct saved in .mat file and
+% filters/removes each row for given criteria. Can save to a new .mat file.
+% Example usage: filter AccMM2Genes.mat for A2_List2Genes
+%
+% Also, one could use it for existing workspace variables by replacing all
+% occurencies of loadedStruct.(nameOfStruct) with the variable name, BUT
+% it should be easier just to save it with right-click in workspace view
+% and use as intended.
+% 
+%    input:
+%%%%     -- .mat file with struct to load
+%%%%     -- parameters
+%%%%     -- criteria for rows to filter out in line 66
+%    output:
+%%%%     -- filtered .mat file with rows hitting criteria missing
+
+%% settings %%
+
+% the .mat file with a struct to load
+pathOfMatFile = "C:\Users\[username]\...\file.mat";
+% whether to save filtered .mat file
+shallFileBeSaved = true;
+% the path where to save the filtered .mat file
+pathToSave = "C:\Users\[username]\...\file_filtered.mat";
+% name of the struct that was saved/should be filtered
+nameOfStruct = "xxx"; % e.g. "MultiHitStat"
+% field name / column to apply critera on
+fieldToCheck = "xxx"; %e.g. "FracMean"
+
+%%%% CHANGE CRITERIA BELOW %%%%
+%%%% you just have to edit the criteria below this line %%%%
+
+
+%% load struct from .mat file into variable loadedStruct
+try
+    loadedStruct = load(pathOfMatFile);
+% on errors
+catch ME
+    % show error
+    disp(ME);
+    % handle wrong file format
+    if ME.identifier == "MATLAB:load:numColumnsNotSame"
+        error("Error loading file. Is it a valid .mat file?");
+    % handle file missing
+    elseif ME.identifier == "MATLAB:load:couldNotReadFile"
+        error('Error loading file. The path correct? It should end with ".mat"');
+    end
+end
+disp("The file " + pathOfMatFile + " was loaded.")
+
+%% initialize list of rows to delete
+rowsToDelete = [];
+
+%% go through the whole struct (2nd dimenstion of struct size)
+% and check criteria
+for i=1:size(loadedStruct.(nameOfStruct),2);
+    % if this criteria is hit, then mark for deletion
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %%%%%%%% change this criterion as you need it %%%%%%%%%%%%%%%
+    %%%%%%%%      here it is: "equals zero"      %%%%%%%%%%%%%%%%
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    if loadedStruct.(nameOfStruct)(i).(fieldToCheck) == 0
+        % mark for deletion
+        rowsToDelete = [rowsToDelete, uint32(i)];
+    end
+end
+
+%% delete (fill with empty) the marked rows of the struct
+loadedStruct.(nameOfStruct)(rowsToDelete) = [];
+%% print how many rows were deleted
+disp("From " + string(structLengths(2)) + " rows, " ...
+    + string(size(rowsToDelete,2)) + " were deleted.");
+
+%% save new .mat if enabled
+if shallFileBeSaved
+    try
+        save(pathToSave, "-struct", "loadedStruct");
+    % on errors
+    catch ME
+        disp(ME);
+        % handle parent directory missing
+        if ME.identifier == "MATLAB:save:noParentDir"
+            error("Error, the given directory to save the file " + ...
+                "seems to be missing or incorrect.");
+        end
+    end
+    % display if successful
+    disp("Filtered .mat was saved to " + pathToSave);
+else
+    disp("The filtered struct was not saved. You may do it on your " + ...
+        "own using the workspace.");
+end

README.md

@@ -6,6 +6,12 @@ The pipeline is visualized in the following scheme:
 
 <img src="https://github.com/Easybel/DetectionGV/blob/main/Pipeline_WGS.png" width="900">
 
+A more detailed diagram can be found on LucidChart <https://lucid.app/documents/view/fa9f52da-edf4-4fb2-9b6c-d01996f4768e> or under [/documentation](/documentation)
+
+Preview:
+
+<img src="https://github.com/Easybel/DetectionGV/blob/main/documentation/DetectionGV_preview.png" width="900">
+
 # Overview of folders and scripts
 - **[0_WGSPipeline](https://github.com/Easybel/DetectionGV/tree/main/0_WGSPipeline)**  
   - This contains all bioinformatic scripts needed to analyse whole genome, raw sequencing reads of bacterial transformation hybrids.

documentation/DetectionGV.csv

@@ -0,0 +1,209 @@
+Id,Name,Shape Library,Page ID,Contained By,Group,Line Source,Line Destination,Source Arrow,Destination Arrow,Status,Text Area 1,Text Area 2,Text Area 3,Text Area 4,Text Area 5,Text Area 6,Text Area 7,Comments
+1,Document,,,,,,,,,Draft,DetectionGV,,,,,,,
+2,Page,,,,,,,,,,Page 1,,,,,,,
+3,Cloud,Geometric Shapes,2,,,,,,,,3_CombiScriptInsertions.sh,,,,,,,
+4,Cloud,Geometric Shapes,2,,,,,,,,2_CombiScriptSamtools.sh,,,,,,,
+5,Cloud,Geometric Shapes,2,,,,,,,,1_QCScript.sh,,,,,,,
+6,Cloud,Geometric Shapes,2,,,,,,,,0_DicIndex.sh,,,,,,,
+7,DividerBlock,,2,,,,,,,,,,,,,,,
+8,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta    (recipient WT),,,,,,,
+9,Text,Standard,2,,,,,,,,Trimmomatic trimmomatic PE,,,,,,,
+10,Decision,Flowchart Shapes/Containers,2,,,,,,,,raw reads .fastq(.gz) of hybrids,,,,,,,
+11,Text,Standard,2,,,,,,,,Align reads to reference genome (recipient wild type) bwa mem -B 1 -O 1,,,,,,,
+12,Text,Standard,2,,,,,,,,FastQC fastqc,,,,,,,
+13,Decision,Flowchart Shapes/Containers,2,,,,,,,,quality reports .zip/.html,,,,,,,
+14,Text,Standard,2,,,,,,,,pile up bcftools mpileup,,,,,,,
+15,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Ref_bcf.vcf,,,,,,,
+16,Text,Standard,2,,,,,,,,calculate coverage with BedTools genomeCoverageBed,,,,,,,
+17,Decision,Flowchart Shapes/Containers,2,,,,,,,,coverage _2Ref_coverage.txt,,,,,,,
+18,Text,Standard,2,,,,,,,,"""Hard"" align reads to donor genome (recipient wild type) bwa mem",,,,,,,
+19,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Donor.sam,,,,,,,
+20,Text,Standard,2,,,,,,,,sort samtools sort,,,,,,,
+21,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Donor_sort.bam,,,,,,,
+22,Text,Standard,2,,,,,,,,index samtools index,,,,,,,
+23,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Donor_sort.bam.bai,,,,,,,
+24,Text,Standard,2,,,,,,,,calculate coverage with BedTools genomeCoverageBed,,,,,,,
+25,Decision,Flowchart Shapes/Containers,2,,,,,,,,coverage _2Donor_coverage.txt,,,,,,,
+26,Text,Standard,2,,,,,,,,Variant calling bcftools call,,,,,,,
+27,Decision,Flowchart Shapes/Containers,2,,,,,,,,variant list _2Ref_bcfcall.vcf,,,,,,,
+28,Display,Flowchart Shapes/Containers,2,,,,,,,,"paths, filenames, sampleType, filter parameters",,,,,,,
+29,Decision,Flowchart Shapes/Containers,2,,,,,,,,SNPSummary.mat,,,,,,,
+30,Text,Standard,2,,,,,,,,A0c_AccessoryGenome.m,,,,,,,
+31,Display,Flowchart Shapes/Containers,2,,,,,,,,"paths, filenames, filter parameters, genome length recipient (.fasta letter count AGTC)",,,,,,,
+32,Sticky note,Sticky Notes,2,,,,,,,,list of single replacements + some metadata,,,,,,,
+33,Sticky note,Sticky Notes,2,,,,,,,,filters single replacements,,,,,,,
+34,Sticky note,Sticky Notes,2,,,,,,,,list of single replacements + their positions -------------------  for each sample,,,,,,,
+35,Sticky note,Sticky Notes,2,,,,,,,,filters ???,,,,,,,
+36,Sticky note,Sticky Notes,2,,,,,,,,list of single replacements + their positions -------------------  for each sample,,,,,,,
+37,Cloud,Geometric Shapes,2,,,,,,,,2_CombiScript Samtools.sh,,,,,,,
+38,Decision,Flowchart Shapes/Containers,2,,,,,,,,.dict (recipient WT),,,,,,,
+39,Cloud,Geometric Shapes,2,,,,,,,,1_QCScript.sh,,,,,,,
+40,Decision,Flowchart Shapes/Containers,2,,,,,,,,raw reads .fastq(.gz) of donor,,,,,,,
+41,Decision,Flowchart Shapes/Containers,2,,,,,,,,(un)paired reads          _P.fastq          _U.fastq,,,,,,,
+42,Decision,Flowchart Shapes/Containers,2,,,,,,,,variant list _2Ref_bcf.vcf,,,,,,,
+43,Delete,Salesforce Architecture Diagrams,2,,,,,,,,,,,,,,,
+44,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta        (donor),,,,,,,
+45,LinkUnfurlBlock,,2,,,,,,,,Basic Local Alignment Search Tool,Nih,,,,,,
+46,Text,Standard,2,,,,,,,,A0d_Multimapper.m,,,,,,,
+47,Text,Standard,2,,,,,,,,2x,,,,,,,
+48,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta        (recipient WT),,,,,,,
+49,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta        (recipient WT),,,,,,,
+50,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta        (recipient WT),,,,,,,
+51,Decision,Flowchart Shapes/Containers,2,,,,,,,,.fasta        (donor),,,,,,,
+52,Decision,Flowchart Shapes/Containers,2,,,,,,,,hittable (text),,,,,,,
+53,Decision,Flowchart Shapes/Containers,2,,,,,,,,hitttable (text),,,,,,,
+54,Right arrow,Geometric Shapes,2,,,,,,,,"""simulates"" hybrid with 100% transfer",,,,,,,
+55,Decision,Flowchart Shapes/Containers,2,,,,,,,,mm_list.txt,,,,,,,
+56,Decision,Flowchart Shapes/Containers,2,,,,,,,,mm.txt,,,,,,,
+57,Text,Standard,2,,,,,,,,A0b_MasterListFiltering.m,,,,,,,
+58,Decision,Flowchart Shapes/Containers,2,,,,,,,,acc..._allBP.txt,,,,,,,
+59,Decision,Flowchart Shapes/Containers,2,,,,,,,,acc..._allBP.mat,,,,,,,
+60,Decision,Flowchart Shapes/Containers,2,,,,,,,,master list ml....mat,,,,,,,
+61,Decision,Flowchart Shapes/Containers,2,,,,,,,,master list  ml...txt,,,,,,,
+62,Text,Standard,2,,,,,,,,A1_SNP2CNP.m,,,,,,,
+63,Decision,Flowchart Shapes/Containers,2,,,,,,,,CNPSummary.mat,,,,,,,
+64,Cloud,Geometric Shapes,2,,,,,,,,2_CombiScript Samtools.sh,,,,,,,
+65,Decision,Flowchart Shapes/Containers,2,,,,,,,,.dict (recipient WT),,,,,,,
+66,Cloud,Geometric Shapes,2,,,,,,,,1_QCScript.sh,,,,,,,
+67,Decision,Flowchart Shapes/Containers,2,,,,,,,,raw reads .fastq(.gz) of recipient,,,,,,,
+68,Decision,Flowchart Shapes/Containers,2,,,,,,,,(un)paired reads          _P.fastq          _U.fastq,,,,,,,
+69,Decision,Flowchart Shapes/Containers,2,,,,,,,,SNP artefacts ReciWT_2Ref_ bcfcall.vcf,,,,,,,
+70,Right arrow,Geometric Shapes,2,,,,,,,,"""simulates"" hybrid with 0% transfer",,,,,,,
+71,DividerBlock,,2,,,,,,,,,,,,,,,
+72,Text,Standard,2,,,,,,,,Create dictionary picard.jar CreateSequenceDictionary,,,,,,,
+73,DividerBlock,,2,,,,,,,,,,,,,,,
+74,Text,Standard,2,,,,,,,,2x,,,,,,,
+75,Text,Standard,2,,,,,,,,A0_VariantFiltering.m,,,,,,,
+76,Decision,Flowchart Shapes/Containers,2,,,,,,,,SNP artefact list _ArteSNPs.mat,,,,,,,
+77,Delete,Salesforce Architecture Diagrams,2,,204,,,,,,,,,,,,,
+78,Text,Standard,2,,204,,,,,,"bcf, sam, bam",,,,,,,
+79,Delete,Salesforce Architecture Diagrams,2,,205,,,,,,,,,,,,,
+80,Text,Standard,2,,205,,,,,,"bcfcall, sam, bam, txt",,,,,,,
+81,Decision,Flowchart Shapes/Containers,2,,,,,,,,(un)paired reads        _P.fastq _U.fastq,,,,,,,
+82,Text,Standard,2,,,,,,,,"A3_Cov2DelDup.m
+finds deletions + duplications     based on coverage",,,,,,,
+83,Sticky note,Sticky Notes,2,,,,,,,,how frequently a certain locus was read,,,,,,,
+84,Decision,Flowchart Shapes/Containers,2,,206,,,,,,,,,,,,,
+85,Decision,Flowchart Shapes/Containers,2,,206,,,,,,,,,,,,,
+86,Decision,Flowchart Shapes/Containers,2,,206,,,,,,(un)paired reads        _P.fastq _U.fastq,,,,,,,
+87,Decision,Flowchart Shapes/Containers,2,,,,,,,,artefacts _ArteCov.txt,,,,,,,
+88,Decision,Flowchart Shapes/Containers,2,,,,,,,,_DelDup _sample.mat,,,,,,,
+89,Text,Standard,2,,,,,,,,"A4_Cov2Ins.m
+finds insertions based on coverage",,,,,,,
+90,Decision,Flowchart Shapes/Containers,2,,,,,,,,AccMM2Genes.mat,,,,,,,
+91,Sticky note,Sticky Notes,2,,,,,,,,"Load existing .mat and empty all cells (empty_AccMM2Genes.mat). Run A2_List2Genes.m in txtListStartEnd-mode with acc..._allBP.txt as far as possible, skip/fix possible errors until MultiHitStat is generated. Save as .mat and filter for FracMean > 0 (e.g. use FilterStructArray_by_PH.m). ",,,,,,,
+92,Text,Standard,2,,,,,,,,A2_List2Genes.m,,,,,,,
+93,Decision,Flowchart Shapes/Containers,2,,,,,,,,bed file ...bed.mat,,,,,,,
+94,Cloud Deployment Manager,Google Cloud Platform 2021,2,,,,,,,,plots,,,,,,,
+95,Decision,Flowchart Shapes/Containers,2,,,,,,,,.dict (recipient WT),,,,,,,
+96,Decision,Flowchart Shapes/Containers,2,,,,,,,,.dict (donor),,,,,,,
+97,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Ref.sam,,,,,,,
+98,Text,Standard,2,,,,,,,,sort samtools sort,,,,,,,
+99,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Ref_sort.bam,,,,,,,
+100,Text,Standard,2,,,,,,,,index samtools index,,,,,,,
+101,Decision,Flowchart Shapes/Containers,2,,,,,,,,_2Ref_sort.bam.bai,,,,,,,
+102,Display,Flowchart Shapes/Containers,2,,,,,,,,"paths, filenames, filter parameters, genome length recipient (.fasta letter count AGTC)",,,,,,,
+103,Cloud Deployment Manager,Google Cloud Platform 2021,2,,,,,,,,plots,,,,,,,
+104,Display,Flowchart Shapes/Containers,2,,,,,,,,"paths, filenames, filter parameters, genome length recipient (.fasta letter count AGTC)",,,,,,,
+105,Diagram key,Standard,2,,,,,,,,Legend,recipient file,donor file,reciprocal hybrid (recipient/donor) file,hybrid (donor/recipient) file,Matlab program (.m) or bash command,bash file,
+106,Line,,2,,,8,72,None,Arrow,,,,,,,,,
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+108,Line,,2,,,10,9,None,Arrow,,,,,,,,,
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+206,Group 3,,2,,,,,,,,,,,,,,,

documentation/README.md

@@ -0,0 +1,4 @@
+The diagram was created with LucidChart. Unfortunately this is closed and some featurs are premium only, so it is a kind of vendor lock-in. I can share the diagram to your LucidChart account, otherwise feel free to rebuild it from the given files.
+<https://lucid.app/documents/view/fa9f52da-edf4-4fb2-9b6c-d01996f4768e>
+
+ <p xmlns:cc="http://creativecommons.org/ns#" >This diagram is marked with <a href="http://creativecommons.org/publicdomain/zero/1.0?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC0 1.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/zero.svg?ref=chooser-v1"></a> and dedicated to the public domain.</p>