def meme(self):
"""promoter detectopn"""
print("Running promoter detection")
self.check_multi_files(
[self._args.tss_files, self._args.fasta_files],
["--tss_files", "--fasta_files"])
if not self._args.tss_source:
self.check_multi_files([self._args.annotation_files],
["--annotation_files"])
if (self._args.program == "both") or (
self._args.program == "meme"):
self._args.meme_path = self.check_execute_file(self._args.meme_path)
elif (self._args.program == "both") or (
self._args.program == "glam2"):
self._args.glam2_path = self.check_execute_file(self._args.glam2_path)
project_creator.create_subfolders(
self._paths.required_folders("promoter"))
args_pro = self.args_container.container_promoter(
self._args.meme_path, self._args.glam2_path,
self._paths.promoter_output_folder, self._args.tex_libs,
self._args.tss_files, self._args.fasta_files,
self._args.num_motifs, self._args.nt_before_tss,
self._args.motif_width, self._args.tss_source,
self._args.annotation_files, self._args.end_run,
self._args.combine_all, self._args.e_value,
self._args.parallels, self._args.program)
meme = MEME(args_pro)
meme.run_meme(args_pro)
class TestMEME(unittest.TestCase):
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.out_folder = "test_folder/output"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out_folder)
os.mkdir(os.path.join(self.out_folder, "fasta_output"))
self.tss_folder = os.path.join(self.test_folder, "tss_folder")
if (not os.path.exists(self.tss_folder)):
os.mkdir(self.tss_folder)
self.gff_folder = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gff_folder)):
os.mkdir(self.gff_folder)
self.fa_folder = os.path.join(self.test_folder, "fa_folder")
if (not os.path.exists(self.fa_folder)):
os.mkdir(self.fa_folder)
args = self.mock_args.mock()
args.tsss = self.tss_folder
args.fastas = self.fa_folder
args.gffs = self.gff_folder
args.output_folder = self.out_folder
self.meme = MEME(args)
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_move_and_merge_fasta(self):
me.del_repeat_fasta = Mock_func().mock_del_repeat_fasta
if (not os.path.exists("tmp")):
os.mkdir("tmp")
gen_file("tmp/primary.fa", "primary")
gen_file("tmp/secondary.fa", "secondary")
gen_file("tmp/internal.fa", "internal")
gen_file("tmp/antisense.fa", "antisense")
gen_file("tmp/orphan.fa", "orphan")
self.meme._move_and_merge_fasta(self.test_folder, "test")
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_all_types.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_primary.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_secondary.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_internal.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_antisense.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_orphan.fa")))
self.assertTrue(os.path.exists(os.path.join(self.test_folder, "test_allstrain_without_orphan.fa")))
def test_split_fasta_by_strain(self):
with open(os.path.join(self.fa_folder, "allstrain.fa"), "w") as fh:
fh.write(""">aaa_aaa_aaa
ATTATATATA
>bbb_bbb_bbb
AATTAATTAA""")
self.meme._split_fasta_by_strain(self.fa_folder)
self.assertTrue(os.path.join(self.fa_folder, "aaa.fa"))
self.assertTrue(os.path.join(self.fa_folder, "bbb.fa"))
def meme(self):
"""promoter detectopn"""
print("Running promoter detection...")
self.check_folder([self._args.TSS_folder, self._args.fasta_folder])
if not self._args.TSS_source:
self.check_folder([self._args.annotation_folder])
project_creator.create_subfolders(
self._paths.required_folders("promoter"))
args_pro = self.args_container.container_promoter(
self._args.MEME_path,
self._paths.promoter_output_folder, self._args.tex_libs,
self._args.TSS_folder, self._args.fasta_folder,
self._args.num_motif, self._args.nt_before_TSS,
self._args.motif_width, self._args.TSS_source,
self._args.tex_wig_path, self._args.annotation_folder,
self._args.combine_all, self._args.e_value)
meme = MEME(args_pro)
meme.run_meme(args_pro)
def meme(self):
"""promoter detectopn"""
print("Running promoter detection...")
self.check_folder([self._args.TSS_folder, self._args.fasta_folder])
if not self._args.TSS_source:
self.check_folder([self._args.annotation_folder])
project_creator.create_subfolders(
self._paths.required_folders("promoter"))
args_pro = self.args_container.container_promoter(
self._args.MEME_path, self._paths.promoter_output_folder,
self._args.tex_libs, self._args.TSS_folder,
self._args.fasta_folder, self._args.num_motif,
self._args.nt_before_TSS, self._args.motif_width,
self._args.TSS_source, self._args.tex_wig_path,
self._args.annotation_folder, self._args.combine_all,
self._args.e_value)
meme = MEME(args_pro)
meme.run_meme(args_pro)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.out_folder = "test_folder/output"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out_folder)
os.mkdir(os.path.join(self.out_folder, "fasta_output"))
self.tss_folder = os.path.join(self.test_folder, "tss_folder")
if (not os.path.exists(self.tss_folder)):
os.mkdir(self.tss_folder)
self.gff_folder = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gff_folder)):
os.mkdir(self.gff_folder)
self.fa_folder = os.path.join(self.test_folder, "fa_folder")
if (not os.path.exists(self.fa_folder)):
os.mkdir(self.fa_folder)
args = self.mock_args.mock()
args.tsss = self.tss_folder
args.fastas = self.fa_folder
args.gffs = self.gff_folder
args.output_folder = self.out_folder
self.meme = MEME(args)
def setUp(self):
self.mock_args = MockClass()
self.test_folder = "test_folder"
self.out_folder = "test_folder/output"
if (not os.path.exists(self.test_folder)):
os.mkdir(self.test_folder)
os.mkdir(self.out_folder)
os.mkdir(os.path.join(self.out_folder, "fasta_output"))
self.tss_folder = os.path.join(self.test_folder, "tss_folder")
if (not os.path.exists(self.tss_folder)):
os.mkdir(self.tss_folder)
self.gff_folder = os.path.join(self.test_folder, "gff_folder")
if (not os.path.exists(self.gff_folder)):
os.mkdir(self.gff_folder)
self.fa_folder = os.path.join(self.test_folder, "fa_folder")
if (not os.path.exists(self.fa_folder)):
os.mkdir(self.fa_folder)
args = self.mock_args.mock()
args.tsss = self.tss_folder
args.fastas = self.fa_folder
args.gffs = self.gff_folder
args.output_folder = self.out_folder
self.meme = MEME(args)