Adds a field test and data

Author: StuntsPT

tests/alstructure_field_tests.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# Copyright 2019 Francisco Pina Martins <[email protected]>
+# This file is part of structure_threader.
+# structure_threader is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# structure_threader is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with structure_threader. If not, see <http://www.gnu.org/licenses/>.
+
+set -e
+
+LightGreen='\033[1;32m'
+NoColor='\033[0m'
+
+echo "Runnig ALStructure 'field test'. This will simulate a full wrapped run on small test data."
+
+git_dir=$(pwd)
+str_bin=$(which alstructure_wrapper.R)
+structure_threader_exec=$(which structure_threader)
+
+tar xvfJ ${git_dir}/tests/smalldata/BigTestData.bed.tar.xz -C ${git_dir}/tests/smalldata/
+${structure_threader_exec} run -i ${git_dir}/tests/smalldata/BigTestData.bed -o ~/results_als -als ${str_bin} -K 4 -t 4 --ind ${git_dir}/tests/smalldata/indfile.txt
+
+echo -e "${LightGreen}ALStructure 'Field test' ran successfully. Yay!${NoColor}"