#!/usr/bin/env python3 import os import inspect import unittest import logging import shutil import bt2face import dataface import btdata from optparse import OptionParser class TestRegressions(unittest.TestCase): """ Main regression fixture. """ def test_288(self): """ Check if --un option works correctly when used with --no-unal """ # run --un and record unaligned file size and orig file size # run --no-unal and record file size # check if --no-unali + --un files size equal the orig file size out_sam = 'test288_out.sam' not_algn = 'test288_nal.fastq' ref_index = os.path.join(g_bdata.index_dir_path,'lambda_virus') reads = os.path.join(g_bdata.reads_dir_path,'longreads.fq') args = "--quiet -x %s -U %s -a --un %s -S %s" % (ref_index,reads,not_algn,out_sam) ret = g_bt.run(args) self.assertEqual(ret,0) sam_size = dataface.SamFile(out_sam).size() no_algn_size = dataface.FastaQFile(not_algn).size() args = "--quiet -x %s -U %s -a --un %s --no-unal -S %s" % (ref_index,reads,not_algn,out_sam) ret = g_bt.run(args) self.assertEqual(ret,0) no_al_sam_size = dataface.SamFile(out_sam).size() self.assertEqual(no_al_sam_size + no_algn_size, sam_size) os.remove(out_sam) os.remove(not_algn) def test_279(self): """ Check if --un-conc option works correctly when used with --no-unal """ out_no_conc = 'test279_nconc.fq' out_conc = 'test279_conc.fq' out_sam = 'test279.sam' out_p1_nc = 'test279_nconc.1.fq' out_p2_nc = 'test279_nconc.2.fq' out_p1_conc = 'test279_conc.1.fq' out_p2_conc = 'test279_conc.2.fq' ref_index = os.path.join(g_bdata.index_dir_path,'lambda_virus') pairs_1 = os.path.join(g_bdata.reads_dir_path,'reads_1.fq') pairs_2 = os.path.join(g_bdata.reads_dir_path,'reads_2.fq') args = "--quiet -x %s -1 %s -2 %s --un-conc %s --dovetail --al-conc %s -S %s" % (ref_index,pairs_1,pairs_2,out_no_conc,out_conc,out_sam) ret = g_bt.run(args) self.assertEqual(ret,0) conc_p1_size_step1 = dataface.FastaQFile(out_p1_conc).size() conc_p2_size_step1 = dataface.FastaQFile(out_p2_conc).size() nc_p1_size_step1 = dataface.FastaQFile(out_p1_nc).size() nc_p2_size_step1 = dataface.FastaQFile(out_p2_nc).size() self.assertEqual(conc_p1_size_step1, conc_p2_size_step1, "Number of concordant sequences in pass 1 should match.") self.assertEqual(nc_p1_size_step1, nc_p2_size_step1, "Number of non-concordant sequences in pass 1 should match.") args = "--quiet -x %s -1 %s -2 %s --no-unal --un-conc %s --dovetail --al-conc %s -S %s" % (ref_index,pairs_1,pairs_2,out_no_conc,out_conc,out_sam) ret = g_bt.run(args) self.assertEqual(ret,0) conc_p1_size_step2 = dataface.FastaQFile(out_p1_conc).size() conc_p2_size_step2 = dataface.FastaQFile(out_p2_conc).size() nc_p1_size_step2 = dataface.FastaQFile(out_p1_nc).size() nc_p2_size_step2 = dataface.FastaQFile(out_p2_nc).size() self.assertEqual(conc_p1_size_step2, conc_p2_size_step2, "Number of concordant sequences in pass 2 should match.") self.assertEqual(nc_p1_size_step2, nc_p2_size_step2, "Number of non-concordant sequences in pass 2 should match.") self.assertEqual(conc_p1_size_step1, conc_p1_size_step2, "Number of concordant sequences in both steps should match.") self.assertEqual(conc_p2_size_step1, conc_p2_size_step2, "Number of concordant sequences in both steps should match.") self.assertEqual(nc_p1_size_step1, nc_p1_size_step2, "Number of non-concordant sequences in both steps should match.") self.assertEqual(nc_p2_size_step1, nc_p2_size_step2, "Number of non-concordant sequences in both steps should match.") self.assertTrue(1,"temp") os.remove(out_p1_conc) os.remove(out_p2_conc) os.remove(out_p1_nc) os.remove(out_p2_nc) os.remove(out_sam) def test_version(self): """ Check if --version option works correctly. """ args = "--version" ret = g_bt.silent_run(args) self.assertEqual(ret,0) def test_x_option(self): """ Check if -x is indeed mandatory. """ ref_index = os.path.join(g_bdata.index_dir_path,'lambda_virus') reads = os.path.join(g_bdata.reads_dir_path,'longreads.fq') out_sam = 'test_x_option.sam' args = "%s -U %s -S %s " % (ref_index,reads,out_sam) ret = g_bt.silent_run(args) self.assertNotEqual(ret,0) args = "-x %s -U %s -S %s " % (ref_index,reads,out_sam) ret = g_bt.silent_run(args) self.assertEqual(ret, 0) os.remove(out_sam) def test_313(self): """ Check if --un-conc, --al-conc, --un, --al do not fail in case of a dot character present in their path name. """ ref_index = os.path.join(g_bdata.index_dir_path,'lambda_virus') pairs_1 = os.path.join(g_bdata.reads_dir_path,'reads_1.fq') pairs_2 = os.path.join(g_bdata.reads_dir_path,'reads_2.fq') no_dot_dir = 'nodotdir' dot_dir = 'v.12_.test' un_basename = 'bname' out_spec = os.path.join(no_dot_dir,un_basename) out_spec_dot= os.path.join(dot_dir,un_basename) args = "--quiet -x %s -1 %s -2 %s --un-conc %s -S %s" % (ref_index,pairs_1,pairs_2,out_spec,os.devnull) try: os.makedirs(no_dot_dir) os.makedirs(dot_dir) except: pass ret = g_bt.silent_run(args) self.assertEqual(ret, 0) mate1_count = dataface.FastaQFile(out_spec + '.1').size() args = "--quiet -x %s -1 %s -2 %s --un-conc %s -S %s" % (ref_index,pairs_1,pairs_2,out_spec_dot,os.devnull) ret = g_bt.silent_run(args) self.assertEqual(ret, 0, "--un-conc should work with dots in its path.") mate1_count_dot = dataface.FastaQFile(out_spec_dot + '.1').size() self.assertEqual(mate1_count, mate1_count_dot, "Number of seqs should be the same.") args = "--quiet -x %s -1 %s -2 %s --un-conc %s -S %s" % (ref_index,pairs_1,pairs_2,dot_dir,os.devnull) ret = g_bt.silent_run(args) self.assertEqual(ret, 0, "--un-conc should work with a path only.") mate1_fs = os.path.join(dot_dir,"un-conc-mate.1") self.assertTrue(os.path.isfile(mate1_fs), "--un-conc output is missing for path only case.") mate1_count_dot_only = dataface.FastaQFile(mate1_fs).size() self.assertEqual(mate1_count, mate1_count_dot_only, "Number of seqs should be the same.") args= "--quiet -x %s -1 %s -2 %s --un-conc %s --al-conc %s --un %s -S %s" % (ref_index,pairs_1,pairs_2,dot_dir,dot_dir,dot_dir,os.devnull) ret = g_bt.run(args) self.assertEqual(ret, 0) mate1_al = os.path.join(dot_dir,"al-conc-mate.1") mate1_un = os.path.join(dot_dir,"un-seqs") self.assertTrue( os.path.isfile(mate1_fs) and os.path.isfile(mate1_al) and os.path.isfile(mate1_un), "--un-conc, --al-conc and --un should not clobber" ) shutil.rmtree(no_dot_dir) shutil.rmtree(dot_dir) def get_suite(): loader = unittest.TestLoader() return loader.loadTestsFromTestCase(TestRegressions) def parse_args(): usage = " %prog [options] \n\n" usage += "Some regression tests.\n" parser = OptionParser(usage=usage) parser.add_option("-v", "--verbose", action="store_true",dest="verbose", default=False, help="Print more info about each test.") (options, args) = parser.parse_args() return options g_bdata = None g_bt = None if __name__ == "__main__": logging.basicConfig(format='%(levelname)s:%(message)s',level=logging.ERROR) options = parse_args() runner = unittest.TextTestRunner() if options.verbose: logging.getLogger().setLevel(level=logging.INFO) runner = unittest.TextTestRunner(verbosity=2) src_file_path = os.path.realpath(inspect.getsourcefile(parse_args)) curr_path = os.path.dirname(src_file_path) bw2_subdir = 'bowtie2' i = curr_path.find(bw2_subdir) bt2_path = curr_path[:i+len(bw2_subdir)] g_bdata = btdata.ExampleData(bt2_path) g_bt = bt2face.BowtieSuite(bt2_path) runner.run(get_suite())