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#!/usr/bin/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())
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