Add regix test script

gitter-lab · Nov 12, 2021 · 37d672d · 37d672d
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diff --git a/data1/README.md b/data1/README.md
@@ -1,9 +1,10 @@
 # ESC to Endoderm Differentiation Dataset
 This directory contains the following files related to the ESC to Endoderm Differentiation dataset.
 
-- **gene_list.mat:** list of 100 genes in the dataset.
+- **gene_list.mat:** list of the names of the 100 genes in the dataset.
 - **X_SCODE_data.mat:** Pre-processed version of expression data corresponding to the genes in gene_list.mat from 356 pseudotime-ordered cells.
-- **X_BranchTest.mat:** An alternative version of the expression data that is used only for SINGE test cases.
+- **X_BranchTest.mat:** An alternative version of the expression data that is used only for SINGE test cases with branching processes.
+- **X_regix_test.mat:** An alternative version of the expression data that is used only for SINGE test cases with regulator indices.
 
 The sources to cite for this dataset are:
 - [Matsumoto et al. 2017](https://academic.oup.com/bioinformatics/article/33/15/2314/3100331), [dataset](https://github.com/hmatsu1226/SCODE/tree/master/data)

diff --git a/tests/standalone_branching_test.sh b/tests/standalone_branching_test.sh
@@ -10,7 +10,7 @@ reducedhyperparams=tests/reduced_hyperparameters.txt
 cat $hyperparams | sed -n '3p' > $reducedhyperparams
 
 # Run SINGE on the example data and inspect the output
-echo Testing SINGE standalone mode in Dockerized SINGE.sh
+echo Testing SINGE standalone mode in Dockerized SINGE.sh with a branching dataset
 output=branching_output
 
 docker run -v $(pwd):/SINGE -w /SINGE agitter/singe:tmp \

diff --git a/tests/standalone_regix_test.sh b/tests/standalone_regix_test.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+# Run SINGE on a dataset with regulator indices specified in standalone mode using the Docker image
+# The regix list is [41, 42] which corresponds to genes SIX1 and RARG
+# Only those two genes should have outgoing edges and non-zero influence scores.
+set -o errexit
+
+# Run SINGE on the example data and inspect the output
+echo Testing SINGE standalone mode in Dockerized SINGE.sh with regulator indices
+hyperparams=tests/example_hyperparameters.txt
+output=regix_output
+
+docker run -v $(pwd):/SINGE -w /SINGE agitter/singe:tmp \
+  standalone data1/X_regix_test.mat data1/gene_list.mat $output $hyperparams
+
+ls $output -l
+
+# Run the tests to evaluate the SINGE outputs from the standalone script
+docker run -v $(pwd):/SINGE -w /SINGE --entrypoint "/bin/bash" agitter/singe:tmp -c \
+  "source ~/.bashrc; conda activate singe-test; tests/compare_example_output.sh $output tests/reference/regix"