Modification for trigenic nature protocol

1. Added supporting trigenic scripts (inside trigenic/) 2. Added test code (test/trigenic_scoring_job.m) and test data (trigenic_scoring_test/) Changes to be committed: modified: Column_Key.md modified: add_SGAPATH.m modified: test/Readme.md new file: test/trigenic_scoring_job.m new file: test/trigenic_scoring_test/raw_triple_test_large.txt.gz new file: test/trigenic_scoring_test/raw_triple_test_small.txt new file: test/trigenic_scoring_test/scored_triple_test_small_digenic.txt.log new file: test/trigenic_scoring_test/scored_triple_test_small_digenic.txt.orf new file: test/trigenic_scoring_test/scored_triple_test_small_digenic.txt.txt new file: test/trigenic_scoring_test/scored_triple_test_small_trigenic.txt new file: test/trigenic_scoring_test/scored_triple_test_small_trigenic.txt_CHROM.pcl
csbio · Apr 1, 2020 · e130d37 · e130d37
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diff --git a/Column_Key.md b/Column_Key.md
@@ -83,3 +83,24 @@ Final format for the 2010 paper
 12. Double mutant fitness
 13. Double mutant fitness standard deviation 
 
+Assignment file for score_trigenic_interactions.m
+-------------------------------------------------
+### 8 col
+1. StrainID1: strain ID of the first single mutant.
+2. ORF1: ORF of the first single mutant.
+3. StrainID2: strain ID of the second single mutant.
+4. ORF2: ORF of the second single mutant.
+5. DMstrainID: strain ID for the double mutant query (ORFs are ORF1 and ORF2).
+6. SM1strainID: strain ID for the single mutant (one of the ORFs will be YDL227C/HO).
+7. SM2strainID: strain ID for the other single mutant.
+8. Annotation: which class this interaction should be assigned to.
+
+Output of print_trigenic.m
+--------------------------
+### 6 col
+1. Query Strain ID
+2. Array Strain ID
+3. Adjusted genetic interaction score (epsilon or tau)
+4. P-value
+5. Double/triple mutant fitness
+6. Double/triple mutant fitness standard deviation
diff --git a/add_SGAPATH.m b/add_SGAPATH.m
@@ -9,5 +9,6 @@ function add_SGAPATH()
    addpath([base_dir '/util']);
    addpath([base_dir '/postprocess']);
    addpath([base_dir '/linkage_est']);
-   addpath([base_dir '/test']);
+   addpath([base_dir '/trigenic']);
+   addpath([base_dir '/test']);   
 end
diff --git a/test/Readme.md b/test/Readme.md
@@ -1,3 +1,6 @@
+SGA score
+===============
+
 Data Description
 ================
 
@@ -53,4 +56,16 @@ test_20.sh diffs the orf file to check for strain census changes
 
 *You may also want to examine a diff of the log files, but as file paths are subject to change
 without affecting scores, this is tricky to do automatically.*
+
 
+Tau-SGA (trigenic) Score
+========================
+
+Data Description
+================
+Data follows the same format of the SGA score. For the trigenic specific test, we have provided two different input files.
+
+1. raw_triple_test_small.txt
+2. raw_triple_test_full.txt.gz
+
+Both files reside inside the directory 'trigenic_scoring_test'. Outputs of different steps for the small dataset is provided inside the directory that include output of the SGA scoring step, Tau-SGA scoring step, and the clustergrams and is generated using the script 'trigenic_scoring_job.m'. The outputs for the full file can be generated with the same script but using the full file as the input instead. 
diff --git a/test/trigenic_scoring_job.m b/test/trigenic_scoring_job.m
@@ -0,0 +1,57 @@
+%% Step 1: Parameter Setup
+
+% A. Mandatory Parameters: provides locations of requried files
+inputfile = 'test/trigenic_scoring_test/raw_triple_test_small.txt'; % unzip raw_triple_test_small.txt.gz
+outputfile= 'test/trigenic_scoring_test/scored_triple_test_small_digenic.txt';
+
+smfitnessfile = 'refdata/smf_DmQueryStd_MiniArray_180208.tsv'; 
+linkagefile = 'refdata/linkage_estimate_curated_160426.txt'; 
+coord_file = 'refdata/chrom_coordinates_150617.tab'; 
+removearraylist = 'refdata/bad_strains_160303.csv'; 
+
+% B. Overridable parameters
+border_strain_orf = 'YOR202W_dma1';
+wild_type = 'URA3control+YDL227C_y13096';
+skip_perl_step = false;
+
+% C. Optional parameters
+% skip_linkage_detection = false;
+% skip_linkage_mask = false;
+% skip_wt_remove = false;
+random_seed = 42; % Reproducibility
+
+
+%% Step 2: Add the SGA repository into path
+
+% Assuming the current directory contains base_dir (relative path); if not, 
+% use the absolute path of the base_dir here
+base_dir = 'SGA_Public-master'; 
+addpath(base_dir);
+
+% Add necessary subdirectories
+add_SGAPATH();
+
+
+%% Step 3: Generate SGA scores
+cd(get_SGAROOT); % Make sure you are inside the base_dir
+compute_sgascore
+
+
+%% Step 4-7: Generate Tau-SGA scores
+
+% Step 4: Load from standard sga output file (12 columns)
+sga = load_sga_epsilon_from_scorefile([outputfile '.txt'], [outputfile '.orf']);
+
+% Step 5: Provide an assignent file (inside SGA_Public-master/refdata)
+assignments = 'assignment_file_170328.csv'; 
+
+% Step 6: Calculate Tau scores (trigenic scores)
+sga_triple = score_trigenic_interactions(sga, assignments);
+
+% Step 7: Print/write the Tau scores
+tau_output_file = strrep(outputfile, 'digenic', 'trigenic');
+print_trigenic(sga, sga, tau_output_file);
+
+
+%% Step 8: Clustering
+generate_fg_clustergram(sga_triple, tau_output_file);
diff --git a/test/trigenic_scoring_test/raw_triple_test_large.txt.gz b/test/trigenic_scoring_test/raw_triple_test_large.txt.gz
diff --git a/test/trigenic_scoring_test/raw_triple_test_small.txt b/test/trigenic_scoring_test/raw_triple_test_small.txt
diff --git a/test/trigenic_scoring_test/scored_triple_test_small_digenic.txt.log b/test/trigenic_scoring_test/scored_triple_test_small_digenic.txt.log
@@ -0,0 +1,145 @@
+Working dir is /home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master
+Using DEFAULT: skip_linkage_detection = false
+Using DEFAULT: skip_linkage_mask = false
+Using DEFAULT: skip_wt_remove = false
+Using DEFAULT: remove_HO_globally = false
+Using DEFAULT: skip_batch_correction = false
+Using DEFAULT: disable_arrayvar_pval = false
+Using DEFAULT: disable_jackknife = false
+Random Seed is 42
+
+Load raw SGA data with batch script: /home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/IO/load_raw_sga_data_withbatch
+
+beginning perl preprocessing
+Data loaded.
+using border strain YOR202W_dma1
+border strain array matches 132544 colonies (19%); expected (19%)
+
+
+Strain Summary:
+type	sn	dma	tsq	damp	tsa	trip	unann	total
+query	0	0	0	0	0	10	0	10
+array	0	1033	0	0	200	0	0	1233
+
+number of unique array plates found: 4
+5232 colonies ignored from "bad arrays"
+
+Constructing plateid->ind map...
+|                                                  |
+|**************************************************|
+Constructing query->ind map...
+Constructing array->ind map...
+
+Linkage filter script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/filter_linkage_colonies
+Linkage Defs: refdata/linkage_estimate_curated_160426.txt
+Chrom   Defs: refdata/chrom_coordinates_150617.tab
+
+Array coordinates mapped. 
+	array orfs matched:   1233
+	array orfs not found: 0
+Query coordinates mapped. 
+	query orfs matched:   0
+	query orfs not found: 10
+All Queries are DM, ...removing HO/URA3 globally...
+Mapping query-specific linkage...
+|                                                  |
+|**************************************************|
+Query Linkage Process Report
+	strain based linkages:	0
+	orf based linkages:	4
+	window based linkages:	6
+	linkage failures:	0
+Mapping array-specific linkage...
+|                                                  |
+|**************************************************|
+Array Linkage Process Report
+	strain based linkages:	11
+	orf based linkages:	0
+	window based linkages:	0
+	linkage failures:	0
+26372 colonies identified as linkage
+
+Plate normalization script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_plate_normalization
+
+Plate normalization...
+|                                                  |
+|**************************************************|
+Calculating colony residuals...
+|                                                  |
+|**************************************************|
+
+Spatial correction script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_spatial_normalization
+
+Spatial normalization...
+|                                                  |
+|**************************************************|
+
+Row/column correction script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_rowcol_normalization
+
+Row/column correction...
+|                                                  |
+|**************************************************|
+
+Competition correction script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_competition_correction
+
+	Get colony neighbor indices script:
+		/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/get_colony_neighbor_indices_list
+
+Mapping neighboring colonies...
+|                                                  |
+|**************************************************|
+
+Competition correction...
+|                                                  |
+|**************************************************|
+
+Plate normalization script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_plate_normalization
+
+Plate normalization...
+|                                                  |
+|**************************************************|
+
+Jackknife variance correction script:
+	/home/mahfuz/Desktop/SGA/Nat_Protocols_Paper_Release/SGA_Public-master/corrections/apply_jackknife_correction
+
+Running the hold-one-out filter...
+|                                                  |
+|**************************************************|
+Finished applying filters...
+Getting arrayplate means...
+|                                                  |
+|**************************************************|
+Preparing for batch normalization...
+|                                                  |
+|**************************************************|
+Batch normalization...
+|                                                  |
+|**************************************************|
+Calculating array WT variance...
+|                                                  |
+|**************************************************|
+Computing average for double mutants...
+|                                                  |
+|*********************************************|
+Pooling across arrayplates for each query...
+|                                                  |
+|************************* -- query_arrplate_vars space reallocation --
+*************************|
+Fitness file report:
+	Exact match	: 1237
+	Partial Match	: 0
+	Not Found	: 6
+	NaN in file	: 55
+Model fitting...
+|                                                  |
+|**************************************************|
+Printing output file...
+|                                                  |
+|**************************************************|
+total time elapsed: 0.06 hours