def test_homGeneMapping_without_hints(self):
'''
test without hints
gtffilenames_without_hints.tbl - is gtffilenames.tbl with hints removed
.../bin/homGeneMapping --noDupes --gtfs=.../gtffilenames_without_hints.tbl
--halfile=aln.hal --tmpdir=.../tmp --outdir=...//outdir
--printHomologs=.../homologs.txt > .../homGeneMapping.out)
'''
os.chdir(os.path.join(default_wd, testdir))
refdir = os.path.join(referencedir, 'without_hints')
outputdir = os.path.join(resultdir, 'without_hints')
aug_path.mkdir_if_not_exists(refdir)
aug_path.mkdir_if_not_exists(outputdir)
resfile = os.path.join(outputdir, 'homGeneMapping.out')
args = '--noDupes --gtfs=' + gtffilenames_without_hints + ' --halfile=aln.hal \
--tmpdir=' + outputdir + '/tmp --outdir=' + outputdir + '/outdir \
--printHomologs=' + outputdir + '/homologs.txt'
aug_process.execute(self, hgmbin + ' ' + args, resfile)
# compare results
if TestHomGeneMapping.opt_compare:
aug_assertions.assertEqualDirectory(self, refdir, outputdir,
TestHomGeneMapping.opt_html,
htmldir)
def test_homGeneMapping_with_sql_hints(self):
'''
test with hints provided by SQLite databaseX
.../bin/homGeneMapping --noDupes --gtfs=.../gtffilenames_without_hints.tbl
--dbaccess=.../homGeneMapping_hints.db --halfile=aln.hal
--tmpdir=.../tmp --outdir=.../outdir
--printHomologs=.../homologs.txt > .../homGeneMapping.out
'''
os.chdir(os.path.join(default_wd, testdir))
refdir = os.path.join(referencedir, 'with_hints')
outputdir = os.path.join(resultdir, 'with_sql_hints')
aug_path.mkdir_if_not_exists(refdir)
aug_path.mkdir_if_not_exists(outputdir)
resfile = os.path.join(outputdir, 'homGeneMapping.out')
args = f'--noDupes --gtfs={gtffilenames_without_hints} \
--dbaccess={sqlitedb} --halfile=aln.hal \
--tmpdir={outputdir}/tmp --outdir={outputdir}/outdir \
--printHomologs={outputdir}/homologs.txt'
aug_process.execute(self, f'{hgmbin} {args}', resfile)
# compare results
if TestHomGeneMapping.opt_compare:
aug_assertions.assertEqualDirectory(self, refdir, outputdir,
TestHomGeneMapping.opt_html,
htmldir)
def test_bam2hints_pipes(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, testfilename)
reffile = os.path.join(referencedir, reffilename)
resfile = os.path.join(resultdir, reffilename)
aug_process.execute(self, f'cat {testfile} | {bam2hintsbin}', resfile)
# compare results
if TestBam2Hints.opt_compare:
aug_assertions.assertEqualFiles(self, reffile, resfile,
TestBam2Hints.opt_html, htmldir)
os.remove(resfile)
def test_bam2wig(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, exampletestfile)
reffile = os.path.join(referencedir, 'test.s.wig')
resfile = os.path.join(resultdir, 'test.s.wig')
aug_process.execute(
self, f'{bam2wigbin} {testfile} | grep -v track', resfile)
# compare results
if TestBam2Wig.opt_compare:
aug_assertions.assertEqualFiles(
self, reffile, resfile, TestBam2Wig.opt_html, htmldir)
os.remove(resfile)
def setUpClass(cls):
os.chdir(default_wd)
clean(force_tmp_dir=False, force_html_dir=True, force_result_dir=True)
aug_path.mkdir_if_not_exists(resultdir)
aug_path.mkdir_if_not_exists(tmpdir)
inputfile = os.path.join(exampledir, exampletestfile)
testfile = os.path.join(tmpdir, exampletestfile)
shutil.copyfile(inputfile, testfile)
os.chdir(tmpdir)
aug_process.execute(None, 'samtools index ' + exampletestfile)
if os.path.isfile(os.path.join(tmpdir, f'{exampletestfile}.bai')):
assert False, 'Test file not indexed.'
def test_bam2wig_region(self):
os.chdir(default_wd)
testfile = os.path.join(tmpdir, exampletestfile)
reffile = os.path.join(referencedir, 'test.s.chr3L.wig')
resfile = os.path.join(resultdir, 'test.s.chr3L.wig')
aug_process.execute(self,
bam2wigbin + ' -t "my_specified_track" -r chr3L ' + testfile + ' | grep -v track',
resfile)
# compare results
if TestBam2Wig.opt_compare:
aug_assertions.assertEqualFiles(
self, reffile, resfile, TestBam2Wig.opt_html, htmldir)
os.remove(resfile)
def test_case(self, testfilename, refsamfilename, filterbamoptions):
os.chdir(default_wd)
testfile = os.path.join(exampledir, testfilename)
refsamfile = os.path.join(referencedir, refsamfilename)
resbamfile = os.path.join(resultdir, refsamfilename + '.bam')
ressamfile = os.path.join(resultdir, refsamfilename)
aug_process.execute(self, binfilterbam + ' --in ' + testfile + ' --out ' + resbamfile + ' ' + filterbamoptions)
if "--no-PG" in aug_process.execute(None, 'samtools view -?'):
aug_process.execute(None, 'samtools view -h --no-PG ' + resbamfile + ' -o ' + ressamfile)
else:
aug_process.execute(None, 'samtools view -h ' + resbamfile + ' -o ' + ressamfile)
self.test_compare(refsamfile, resbamfile, ressamfile)
def setUpClass(cls):
os.chdir(default_wd)
clean(force_tmp_dir=False, force_html_dir=True, force_result_dir=True)
aug_path.mkdir_if_not_exists(resultdir)
aug_path.mkdir_if_not_exists(tmpdir)
# create file with gtf filenames without hint file references
aug_process.execute(
None,
'cat ' + gtffilenames_with_hints + ' | sed "s/gtf\\t.*/gtf/g"',
gtffilenames_without_hints)
# create sqllite database
out_load2sqlitedb = os.path.join(tmpdir, 'out_load2sqlitedb.txt')
if os.path.exists(sqlitedb):
os.remove(sqlitedb)
aug_process.execute(
None, load2sqlbin + ' --species=hg19 --dbaccess=' + sqlitedb +
' ' + examplesdir + '/cgp/human.fa', out_load2sqlitedb)
aug_process.execute(
None, load2sqlbin + ' --species=mm9 --dbaccess=' + sqlitedb + ' ' +
examplesdir + '/cgp/mouse.fa', out_load2sqlitedb)
aug_process.execute(
None, load2sqlbin + ' --noIdx --species=hg19 --dbaccess=' +
sqlitedb + ' ' + testdir + '/gtfs/human.hints.gff',
out_load2sqlitedb)
aug_process.execute(
None, load2sqlbin + ' --noIdx --species=mm9 --dbaccess=' +
sqlitedb + ' ' + testdir + '/gtfs/mouse.hints.gff',
out_load2sqlitedb)
aug_process.execute(None,
load2sqlbin + ' --makeIdx --dbaccess=' + sqlitedb,
out_load2sqlitedb)
