test for GRN

tests/0023_GRNrepressilator/README.md

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+# 0023_GRNrepressilator
+
+a gene regulatory network of 3 genes connected in a circle with inhibition (like repressilator)
+
+## tests
+
+- 1D, 3 units, network, GRN
+- cps file reads well
+- network file reads well
+- named output file
+- checks the regulated_by_1 rate law was created
+- checks that there are exactly 3 species
+- checks that noise worked
+- checks no compartments created
+- checks that there are three synthesis reactions

tests/0023_GRNrepressilator/run.sh

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+#!/bin/bash
+
+# work out our folder name
+test=${PWD##*/}          # to assign to a variable
+test=${test:-/}          # to correct for the case where PWD=/
+
+# run sbmodelr
+../../sbmodelr -g G --pn G 0.8 uni --grn-a -1 --grn-h 4 -n ../sources/3circle.gv -o repressilator.cps --ignore-compartments ../sources/GeneExpressionUnit.cps 3 > output
+
+fail=0
+
+# compare output and target
+difference=$(diff output target_stdout)
+if [[ $difference ]]; then
+  printf 'FAIL %s\n' "${test}"
+  fail=1
+fi
+
+# create model summary
+../model_report.py repressilator.cps >/dev/null
+if ! [[ $? = 0 ]]; then
+  printf 'FAIL %s\n' "${test}"
+  exit -1
+fi
+
+# check that there is one rate law for regulation by 1
+if ! grep -Pq "^regulated_by_1\s+V \* \( \( 1 \+ \( 1 \+ a1 \) \* M1 \^ h1 \) \/ \( 1 \+ M1 \^ h1 \) \)" repressilator.summary.txt; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 2"
+fi
+
+# check that there are three species
+n=$(grep -Pc "^G_[123]\s+reactions\s+[0-9]+\.[0-9]+" repressilator.summary.txt)
+if ((n != 3)); then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 4"
+fi
+
+# check that min and max of initial concentrations are different (meaning noise worked!)
+n=$(grep -Po "^G_[123]\s+reactions\s+([0-9]+\.[0-9]+\s)" repressilator.summary.txt | awk '(NR==1){Min=$3;Max=$3};(NR>=2){if(Min>$3) Min=$3;if(Max<$3) Max=$3} END {if(Min<Max) {print 0} else {print 1}}')
+if ((n != 0)) ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 8"
+fi
+
+# check that no new compartments were created
+n=$(grep -Pc "^cell_[123]\s+fixed" repressilator.summary.txt)
+if ((n != 0))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 16"
+fi
+
+# checks that there are three synthesis reactions
+n=$(grep -Pc "synthesis (G_[123])\s+-> \1\;\s+G_[123]\s+regulated_by_1" repressilator.summary.txt)
+if ((n != 3))  ; then
+  printf 'FAIL %s\n' "${test}"
+  let "fail = $fail + 32"
+fi
+
+if [ "$fail" = 0 ] ; then
+  printf 'PASS %s\n' "${test}"
+  rm repressilator.summary.txt output *.cps
+fi
+
+exit $fail

tests/0023_GRNrepressilator/target_stdout

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+Processing ../sources/GeneExpressionUnit.cps
+  Reactions:         2
+  Species:           1	(Reactions: 1, Fixed: 0, Assignment: 0, ODE: 0)
+  Compartments:      1	(Fixed: 1, Assignment: 0, ODE: 0)
+  Global quantities: 0	(Fixed: 0, Assignment: 0, ODE: 0)
+  Events:            0	(Only time-dependent: 0, variable-dependent: 0)
+  Network:           directed	(Nodes: 3, Edges: 3)
+created new model repressilator.cps with a set of 3 replicas of ../sources/GeneExpressionUnit.cps
+