--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_repex_pipeline.py	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,229 @@
+#!/usr/bin/env python3
+'''
+Basic Tarean and RepeatExplorer tests
+'''
+import subprocess
+import tempfile
+import unittest
+import os
+import shutil
+
+def check_for_missing_files(directory, file_list):
+    ''' check if files exists in the directory '''
+    missing_files = []
+    for f in file_list:
+        path = os.path.join(directory, f)
+        if os.path.exists(path):
+            continue
+        else:
+            missing_files.append(f)
+    return missing_files
+
+
+class TestBasic(unittest.TestCase):
+    ''' basic repex-tarean testcase '''
+    EXECUTABLE = "./seqclust"
+
+    # file lists to check
+    FILE_LIST_BASIC = [
+        "./seqclust/clustering/clusters/dir_CL0001/hitsort_part.csv",
+        "./seqclust/clustering/clusters/dir_CL0001/reads.fasta",
+        "./seqclust/clustering/clusters/dir_CL0001/reads_selection.fasta",
+        "./seqclust/clustering/clusters/dir_CL0001/dna_database_annotation.csv",
+        "./seqclust/clustering/clusters/dir_CL0001/graph_layout.GL",
+        "./seqclust/clustering/clusters/dir_CL0001/graph_layout.png",
+        "./seqclust/clustering/clusters/dir_CL0001/graph_layout_tmb.png",
+        "./seqclust/clustering/clusters/dir_CL0001/graph_layout_directed.RData",
+        "./logfile.txt", "./style1.css", "./documentation.html",
+        "./tarean_report.html", "./cluster_report.html",
+        "./summary_histogram.png", "./index.html", "./sequences.db",
+        "./hitsort.db", "./TAREAN_consensus_rank_1.fasta",
+        "./TAREAN_consensus_rank_2.fasta", "./TAREAN_consensus_rank_3.fasta",
+        "./TAREAN_consensus_rank_4.fasta", "./seqclust/clustering/hitsort",
+        "./seqclust/clustering/hitsort.cls"
+    ]
+    FILE_LIST_ASSEMBLY = [
+        "./seqclust/small_clusters_assembly/small_clusters.aln",
+        "./seqclust/small_clusters_assembly/small_clusters.ace",
+        "./seqclust/small_clusters_assembly/small_clusters.fasta"
+    ]
+    FILE_LIST_FILTERING = ["./seqclust/prerun/filter_sequences.fasta"]
+    FILE_LIST_COMPARATIVE = ["COMPARATIVE_ANALYSIS_COUNTS.csv"]
+    FILE_LIST_CUSTOM_DATABASE = [
+        "./seqclust/custom_databases/extra_database",
+        "./seqclust/clustering/clusters/dir_CL0001/custom_db_extra_database_annotation.csv"
+    ]
+    def setUp(self):
+        pass
+
+    # helper function
+    def tarean_run(self, cmd_options, file_list):
+        ''' Basic taren run '''
+        # output goes to tmp directory
+        tmpdir = tempfile.mkdtemp()
+        logfile = tempfile.NamedTemporaryFile(delete=False)
+        print("\n------------------------------------------------------")
+        print("Temp files:")
+        print("   tmpdir : ", tmpdir)
+        print("  logfile : ", logfile.name)
+        print("------------------------------------------------------")
+        print([self.EXECUTABLE] + ['-l', logfile.name, '-v', tmpdir] + cmd_options)
+        p = subprocess.Popen(
+            args=[self.EXECUTABLE] + ['-l', logfile.name, '-v', tmpdir
+                                     ] + cmd_options)
+        p.wait()
+        status = p.returncode
+        missing_files = check_for_missing_files(directory=tmpdir,
+                                                file_list=file_list)
+        if status:
+            # print log file
+            print("Non zero exit status!")
+            with open(logfile.name) as f:
+                print(f.read())
+
+        self.assertEqual(status, 0)
+        self.assertEqual(
+            len(missing_files),
+            0,
+            msg="\n missing files: \n" + "\n".join(missing_files))
+        shutil.rmtree(tmpdir)
+        os.remove(logfile.name)
+
+
+    def test_help(self):
+        '''Test if help option works '''
+        p = subprocess.Popen(args=[self.EXECUTABLE, "-h"],
+                             stdout=subprocess.PIPE)
+        output = str(p.stdout.readlines())
+        p.stdout.close()
+        p.wait()
+        status = p.returncode
+        self.assertRegex(output, "usage")
+        self.assertRegex(output, "optional arguments")
+        self.assertEqual(status, 0)
+
+    def test_basic_no_merging_tarean(self):
+        ''' Basic taren run '''
+        cmd_options = ['-t', '-p', '-s', '6000', 'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
+
+    def test_basic_with_merging_tarean(self):
+        ''' Basic taren run '''
+        cmd_options = ['-t', '-p', '-M', '0.2', '-s', '6000',
+                       'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
+
+
+    def test_basic_with_merging_tarean_dust_off(self):
+        ''' Basic taren run '''
+        cmd_options = ['-t', '-p', '-M', '0.2', '-s', '6000', "-opt", "ILLUMINA_DUST_OFF",
+                       'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
+
+    def test_long_with_merging_tarean(self):
+        '''Using more data with tarean'''
+        cmd_options = ['-t', '-p', '-M', '0.1', '-m', '0.01',
+                       'test_data/LAS_paired_25k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
+
+    def test_long_with_merging2_tarean(self):
+        '''Using more data with tarean 300k reads'''
+        cmd_options = ['-t', '-p', '-M', '0.1', '-m', '0.01',
+                       'test_data/LAS_paired_300k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
+
+    def test_short_comparative_re(self):
+        '''comparative analysis, two species, small run'''
+        cmd_options = ['-P','3', '-p', '-m', '0.01',
+                       'test_data/sequences_comparative.fasta']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_COMPARATIVE)
+
+    # REPEATEXPLORER - full runs
+    def test_basic_no_merging_re(self):
+        ''' Basic taren run '''
+        cmd_options = ['-p', '-s', '6000', 'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+    def test_basic_no_merging_re_diamond(self):
+        ''' Basic taren run '''
+        cmd_options = ['-p', '-s', '6000','-D','DIAMOND', 'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+
+
+    def test_basic_with_merging_re(self):
+        ''' Basic taren run '''
+        cmd_options = ['-p', '-M', '0.2', '-s', '6000',
+                       'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+    def test_long_with_merging_re(self):
+        '''Using more data with tarean'''
+        cmd_options = ['-p', '-M', '0.1', '-m', '0.01',
+                       'test_data/LAS_paired_25k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+    def test_long_with_merging_re_diamond(self):
+        '''Using more data with tarean and using diamond'''
+        cmd_options = ['-p', '-M', '0.1', '-m', '0.01','-D','DIAMOND',
+                       'test_data/LAS_paired_25k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+    def test_long_with_merging2_re(self):
+        '''Using more data with tarean 300k reads'''
+        cmd_options = ['-p', '-M', '0.1', '-m', '0.01',
+                       'test_data/LAS_paired_300k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
+
+    def test_long_with_merging_and_filtering_re(self):
+        '''Using more data with tarean, test of automatic filtering'''
+        cmd_options = ['-A', '-p', '-M', '0.2', '-m', '0.01',
+                       'test_data/ceu_200k.fasta']
+        self.tarean_run(
+            cmd_options,
+            file_list=self.FILE_LIST_BASIC + self.FILE_LIST_FILTERING + self.FILE_LIST_ASSEMBLY)
+
+    def test_custom_database_re(self):
+        ''' Basic taren run '''
+        cmd_options = ['-p', '-d', 'test_data/extra_database', 'extra_database', 'test_data/LAS_paired_10k.fas']
+        self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_CUSTOM_DATABASE)
+
+    def tearDown(self):
+        pass
+
+
+SHORT_TASK_NAME_LIST_TAREAN = ['test_help', 'test_basic_no_merging_tarean',
+                               'test_basic_with_merging_tarean',
+                               'test_basic_with_merging_tarean_dust_off']
+LONG_TASK_NAME_LIST_TAREAN = ['test_long_with_merging_tarean',
+                              'test_long_with_merging2_tarean']
+SHORT_TASK_NAME_LIST_RE = ['test_basic_no_merging_re',
+                           'test_basic_with_merging_re',
+                           'test_basic_no_merging_re_diamond']
+LONG_TASK_NAME_LIST_RE = ['test_long_with_merging_re',
+                          'test_long_with_merging2_re',
+                          'test_long_with_merging_and_filtering_re',
+                          'test_long_with_merging_re_diamond']
+
+COMPARATIVE_LIST = ['test_short_comparative_re']
+CUSTOM_DATABASE_LIST = ['test_short_custom_database']
+
+# Test suites:
+SHORT_TAREAN_SUITE = unittest.TestSuite([TestBasic(i)
+                                   for i in SHORT_TASK_NAME_LIST_TAREAN])
+LONG_TAREAN_SUITE = unittest.TestSuite([TestBasic(i)
+                                  for i in LONG_TASK_NAME_LIST_TAREAN])
+COMPARATIVE_SUITE = unittest.TestSuite([TestBasic(i) for i in COMPARATIVE_LIST])
+CUSTOM_DB_SUITE = unittest.TestSuite([TestBasic('test_custom_database_re')])
+
+SHORT_RE_SUITE = unittest.TestSuite([TestBasic(i) for i in SHORT_TASK_NAME_LIST_RE])
+LONG_RE_SUITE = unittest.TestSuite([TestBasic(i) for i in LONG_TASK_NAME_LIST_RE])
+
+SHORT_SUITE = unittest.TestSuite([SHORT_RE_SUITE, SHORT_TAREAN_SUITE,
+                                  COMPARATIVE_SUITE, CUSTOM_DB_SUITE])
+
+LONG_LONG = unittest.TestSuite([LONG_RE_SUITE, LONG_TAREAN_SUITE])
+
+# for single test tesing
+if __name__ == '__main__':
+    unittest.main(verbosity=2)