def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
commonInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(commonInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir, "5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)
# create multiple dbs
self.blastdbs_multi = []
for db in ['humanChr1Subset.fa', 'humanChr9Subset.fa']:
dbPath = tools.blast.MakeblastdbTool().build_database(
os.path.join(util.file.get_test_input_path(self), db),
os.path.join(self.tempDir, db[:-3]))
self.blastdbs_multi.append(dbPath)
# tar one db, but not the other
tar_db_tgz = util.file.mkstempfname('-humanChr9Subset.blastn.db.tar.gz')
cmd = ['tar', '-C', self.tempDir, '-cvzf', tar_db_tgz]
for ext in ('nhr', 'nin', 'nsq'):
cmd.append('humanChr9Subset.'+ext)
subprocess.check_call(cmd)
self.blastdbs_multi[1] = tar_db_tgz
for ext in ('nhr', 'nin', 'nsq'):
os.unlink(os.path.join(self.tempDir, 'humanChr9Subset.'+ext))
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
commonInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(commonInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, self.database_prefix_path)
# create multiple dbs
self.blastdbs_multi = []
for db in ['humanChr1Subset.fa', 'humanChr9Subset.fa']:
dbPath = tools.blast.MakeblastdbTool().build_database(
os.path.join(util.file.get_test_input_path(self), db),
os.path.join(self.tempDir, db[:-3]))
self.blastdbs_multi.append(dbPath)
# tar one db, but not the other
tar_db_tgz = util.file.mkstempfname(
'-humanChr9Subset.blastn.db.tar.gz')
cmd = ['tar', '-C', self.tempDir, '-cvzf', tar_db_tgz]
for ext in ('nhr', 'nin', 'nsq'):
cmd.append('humanChr9Subset.' + ext)
subprocess.check_call(cmd)
self.blastdbs_multi[1] = tar_db_tgz
for ext in ('nhr', 'nin', 'nsq'):
os.unlink(os.path.join(self.tempDir, 'humanChr9Subset.' + ext))
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
polio_fasta = os.path.join(util.file.get_test_input_path(),
'TestMetagenomicsViralMix', 'db', 'library',
'Viruses', 'Poliovirus_uid15288',
'NC_002058.ffn')
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, self.database_prefix_path)
# create bmtagger db
self.bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(
ref_fasta, self.database_prefix_path + ".bitmask")
self.srprismdb_path = tools.bmtagger.SrprismTool().build_database(
ref_fasta, self.database_prefix_path + ".srprism")
# create last db
self.lastdb_path = tools.last.Lastdb().build_database(
polio_fasta, os.path.join(self.tempDir, 'polio'))
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
self.ebolaRef = util.file.mkstempfname('.fasta', directory=self.tempDir)
shutil.copyfile(os.path.join(util.file.get_test_input_path(), 'G5012.3.fasta'), self.ebolaRef)
self.bwa = tools.bwa.Bwa()
self.samtools = tools.samtools.SamtoolsTool()
self.bwa.index(self.ebolaRef)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
self.ebolaRef = util.file.mkstempfname('.fasta', directory=self.tempDir)
shutil.copyfile(os.path.join(util.file.get_test_input_path(), 'G5012.3.fasta'), self.ebolaRef)
self.bwa = tools.bwa.Bwa()
self.samtools = tools.samtools.SamtoolsTool()
self.bwa.index(self.ebolaRef)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.polio_fasta = os.path.join(
util.file.get_test_input_path(),
'TestMetagenomicsViralMix', 'db', 'library', 'Viruses', 'Enterovirus_C', 'GCF_000861165.1_ViralProj15288_genomic.fna'
)
dbDir = tempfile.mkdtemp()
self.lastdb_path = tools.last.Lastdb().build_database(self.polio_fasta, os.path.join(dbDir, 'NC_002058'))
def setUp(self):
TestCaseWithTmp.setUp(self)
polio_fasta = os.path.join(util.file.get_test_input_path(),
'TestMetagenomicsViralMix', 'db', 'library',
'Viruses', 'Poliovirus_uid15288',
'NC_002058.ffn')
dbDir = tempfile.mkdtemp()
self.lastdb_path = tools.last.Lastdb().build_database(
polio_fasta, os.path.join(dbDir, 'NC_002058'))
def setUp(self):
TestCaseWithTmp.setUp(self)
self.polio_fasta = os.path.join(
util.file.get_test_input_path(), 'TestMetagenomicsViralMix', 'db',
'library', 'Viruses', 'Enterovirus_C',
'GCF_000861165.1_ViralProj15288_genomic.fna')
dbDir = tempfile.mkdtemp()
self.lastdb_path = tools.last.Lastdb().build_database(
self.polio_fasta, os.path.join(dbDir, 'NC_002058'))
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
ref_fasta = os.path.join(util.file.get_test_input_path(),
'5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
taxon_filter.bmtagger_build_db(ref_fasta,
self.tempDir,
"5kb_human_from_chr6",
word_size=8)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
commonInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(commonInputDir, 'TestDepleteHuman',
'5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, self.database_prefix_path)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = os.path.join(util.file.get_test_input_path(),
'TestDepleteHuman')
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
self.bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(
ref_fasta, self.database_prefix_path + ".bitmask")
self.srprismdb_path = tools.bmtagger.SrprismTool().build_database(
ref_fasta, self.database_prefix_path + ".srprism")
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
for db in ['humanChr1Subset', 'humanChr9Subset']:
# .map file is > 100M, so recreate instead of copying
dbfa = os.path.join(myInputDir, db + '.fa')
dbsrprism = os.path.join(self.tempDir, db + '.srprism')
srprismdb_path = tools.bmtagger.SrprismTool().build_database(dbfa, dbsrprism)
# .bitmask and .srprism.* files must be in same dir, so copy
shutil.copy(os.path.join(myInputDir, db + '.bitmask'), self.tempDir)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir, "5kb_human_from_chr6")
# create blast db
self.blastdb_path = classify.blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)
# create bmtagger db
taxon_filter.bmtagger_build_db(ref_fasta, self.tempDir, "5kb_human_from_chr6", word_size=8)
def setUp(self) :
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
srprismPath = tools.bmtagger.SrprismTool().install_and_get_path()
for db in ['humanChr1Subset', 'humanChr9Subset'] :
# .map file is > 100M, so recreate instead of copying
dbfa = os.path.join(myInputDir, db + '.fa')
dbsrprism = os.path.join(self.tempDir, db + '.srprism')
subprocess.check_call([srprismPath, 'mkindex', '-i', dbfa, '-o', dbsrprism])
# .bitmask and .srprism.* files must be in same dir, so copy
shutil.copy(os.path.join(myInputDir, db + '.bitmask'), self.tempDir)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir, "5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)
# create bmtagger db
taxon_filter.bmtagger_build_db(ref_fasta, self.tempDir, "5kb_human_from_chr6", word_size=8)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
srprismPath = tools.bmtagger.SrprismTool().install_and_get_path()
for db in ['humanChr1Subset', 'humanChr9Subset']:
# .map file is > 100M, so recreate instead of copying
dbfa = os.path.join(myInputDir, db + '.fa')
dbsrprism = os.path.join(self.tempDir, db + '.srprism')
subprocess.check_call([srprismPath, 'mkindex', '-i', dbfa, '-o', dbsrprism])
# .bitmask and .srprism.* files must be in same dir, so copy
shutil.copy(os.path.join(myInputDir, db + '.bitmask'), self.tempDir)
def setUp(self) :
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
srprismPath = tools.bmtagger.SrprismTool().install_and_get_path()
for db in ['humanChr1Subset', 'humanChr9Subset'] :
# .map file is > 100M, so recreate instead of copying
dbfa = os.path.join(myInputDir, db + '.fa')
dbsrprism = os.path.join(self.tempDir, db + '.srprism')
assert not os.system(
'{srprismPath} mkindex -i {dbfa} -o {dbsrprism}'.format(
**locals()))
# .bitmask and .srprism.* files must be in same dir, so copy
shutil.copy(os.path.join(myInputDir, db + '.bitmask'), self.tempDir)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
for db in ['humanChr1Subset', 'humanChr9Subset']:
# .map file is > 100M, so recreate instead of copying
dbfa = os.path.join(myInputDir, db + '.fa')
dbsrprism = os.path.join(self.tempDir, db + '.srprism')
srprismdb_path = tools.bmtagger.SrprismTool().build_database(
dbfa, dbsrprism)
# .bitmask and .srprism.* files must be in same dir, so copy
shutil.copy(os.path.join(myInputDir, db + '.bitmask'),
self.tempDir)
def setUp(self):
TestCaseWithTmp.setUp(self)
os.environ.pop('TMPDIR', None)
util.file.set_tmp_dir(None)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, self.database_prefix_path)
# create bmtagger db
self.bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(
ref_fasta, self.database_prefix_path + ".bitmask")
self.srprismdb_path = tools.bmtagger.SrprismTool().build_database(
ref_fasta, self.database_prefix_path + ".srprism")
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
myInputDir = util.file.get_test_input_path(self)
ref_fasta = os.path.join(myInputDir, '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir, "5kb_human_from_chr6")
polio_fasta = os.path.join(
util.file.get_test_input_path(),
'TestMetagenomicsViralMix', 'db', 'library', 'Viruses', 'Poliovirus_uid15288', 'NC_002058.ffn'
)
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(ref_fasta, self.database_prefix_path)
# create bmtagger db
self.bmtooldb_path = tools.bmtagger.BmtoolTool().build_database(ref_fasta, self.database_prefix_path + ".bitmask")
self.srprismdb_path = tools.bmtagger.SrprismTool().build_database(ref_fasta, self.database_prefix_path + ".srprism")
# create last db
self.lastdb_path = tools.last.Lastdb().build_database(polio_fasta, self.database_prefix_path)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
commonInputDir = util.file.get_test_input_path()
ref_fasta = os.path.join(commonInputDir, 'TestDepleteHuman',
'5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir,
"5kb_human_from_chr6")
# create blast db
self.blastdb_path = tools.blast.MakeblastdbTool().build_database(
ref_fasta, self.database_prefix_path)
# create multiple dbs
self.blastdbs_multi = []
for db in ['humanChr1Subset.fa', 'humanChr9Subset.fa']:
dbPath = tools.blast.MakeblastdbTool().build_database(
os.path.join(util.file.get_test_input_path(self), db),
os.path.join(self.tempDir, db[:-3]))
self.blastdbs_multi.append(dbPath)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.tempDir = tempfile.mkdtemp()
ref_fasta = os.path.join(util.file.get_test_input_path(), '5kb_human_from_chr6.fasta')
self.database_prefix_path = os.path.join(self.tempDir, "5kb_human_from_chr6")
taxon_filter.bmtagger_build_db(ref_fasta, self.tempDir, "5kb_human_from_chr6", word_size=8)
def setUp(self):
TestCaseWithTmp.setUp(self)
self.input_dir = util.file.get_test_input_path(self)