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#!/usr/bin/python3
import os
import gzip
import urllib.request, urllib.error, urllib.parse
import inspect
import unittest
import logging
import bt2face
import btdata
import subprocess
from optparse import OptionParser
class TestLargeIndex(unittest.TestCase):
"""
Main fixture for large index testing.
"""
def test_human(self):
wdir = g_bdata.data_dir_path
wdir = os.path.join(wdir,'human')
rdir = g_bdata.reads_dir_path
genome = g_bdata.genomes['human']
genome_fasta = os.path.join(wdir,genome['ref_name'])
genome_index = os.path.join(wdir,'human')
reads = os.path.join(rdir,'human_reads.fa')
ret = g_bt.build("%s human" % genome_fasta)
self.assertEqual(ret,0)
args = "-x %s -f -U %s" % (genome_index,reads)
ret = g_bt.run(args)
self.assertEqual(ret,0)
def test_mouse(self):
wdir = g_bdata.data_dir_path
wdir = os.path.join(wdir,'mouse')
rdir = g_bdata.reads_dir_path
genome = g_bdata.genomes['mouse']
genome_fasta = os.path.join(wdir,genome['ref_name'])
genome_index = os.path.join(wdir,'mouse')
reads = os.path.join(rdir,'mouse_reads.fa')
ret = g_bt.build("%s mouse" % genome_fasta)
self.assertEqual(ret,0)
args = "-x %s -f -U %s" % (genome_index,reads)
ret = g_bt.run(args)
self.assertEqual(ret,0)
def test_large_index(self):
wdir = g_bdata.data_dir_path
wdir = os.path.join(wdir,'ms_hum')
rdir = g_bdata.reads_dir_path
genome = g_bdata.joint_genomes['ms_hum']
genome_fasta = os.path.join(wdir,genome['ref_name'])
genome_index = os.path.join(wdir,'ms_hum')
reads_human = os.path.join(rdir,'human_reads.fa')
reads_mouse = os.path.join(rdir,'mouse_reads.fa')
ret = g_bt.build("%s ms_hum" % genome_fasta)
self.assertEqual(ret,0)
args = "-x %s -f -U %s" % (genome_index,reads_human)
ret = g_bt.run(args)
args = "-x %s -f -U %s" % (genome_index,reads_mouse)
ret = g_bt.run(args)
self.assertEqual(ret,0)
def get_suite():
tests = ['test_human','test_mouse','test_large_index']
return unittest.TestSuite(list(map(TestLargeIndex,tests)))
def parse_args():
usage = " %prog [options] \n\n"
usage += "Warning, this test runs some VERY resource consuming 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.LargeTestsData(bt2_path)
g_bt = bt2face.BowtieSuite(bt2_path)
runner.run(get_suite())
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