def __init__(self, args):
"""Create an instance."""
self._args = args
if (len(args.__dict__) > 3):
if not os.path.exists(args.project_path):
print("Error: --project_path does not exists!")
sys.exit()
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
def setUp(self):
self.test_folder = "test_folder"
if not os.path.exists(self.test_folder):
os.mkdir(self.test_folder)
self.paths = Paths(base_path=self.test_folder)
self.folder_names = [
self.paths.input_folder,
self.paths.output_folder,
self.paths.reference_input_folder,
self.paths.wig_folder,
self.paths.mutation_table_folder,
self.paths.database_folder,
self.paths.manual_TSS_folder,
self.paths.manual_pro_folder,
self.paths.read_folder,
self.paths.bam_folder,
self.paths.target_folder,
self.paths.ratt_folder,
self.paths.tsspredator_folder,
self.paths.utr_folder,
self.paths.transterm_folder,
self.paths.transcript_assembly_output_folder,
self.paths.processing_site_folder,
self.paths.srna_folder,
self.paths.sorf_folder,
self.paths.promoter_output_folder,
self.paths.operon_output_folder,
self.paths.circrna_output_folder,
self.paths.goterm_output_folder,
self.paths.starget_output_folder,
self.paths.snp_output_folder,
self.paths.ppi_output_folder,
self.paths.sublocal_output_folder,
self.paths.ribos_output_folder]
def setUp(self):
self.test_folder = "test_folder"
if not os.path.exists(self.test_folder):
os.mkdir(self.test_folder)
self.paths = Paths(base_path=self.test_folder)
self.folder_names = [
self.paths.input_folder, self.paths.output_folder,
self.paths.reference_input_folder, self.paths.wig_folder,
self.paths.mutation_table_folder, self.paths.database_folder,
self.paths.manual_TSS_folder, self.paths.manual_pro_folder,
self.paths.read_folder, self.paths.bam_folder,
self.paths.target_folder, self.paths.ratt_folder,
self.paths.tsspredator_folder, self.paths.utr_folder,
self.paths.transterm_folder, self.paths.transcript_output_folder,
self.paths.processing_site_folder, self.paths.srna_folder,
self.paths.sorf_folder, self.paths.promoter_output_folder,
self.paths.operon_output_folder, self.paths.circrna_output_folder,
self.paths.goterm_output_folder, self.paths.starget_output_folder,
self.paths.snp_output_folder, self.paths.ppi_output_folder,
self.paths.sublocal_output_folder, self.paths.ribos_output_folder
]
class TestPaths(unittest.TestCase):
def setUp(self):
self.test_folder = "test_folder"
if not os.path.exists(self.test_folder):
os.mkdir(self.test_folder)
self.paths = Paths(base_path=self.test_folder)
self.folder_names = [
self.paths.input_folder, self.paths.output_folder,
self.paths.reference_input_folder, self.paths.wig_folder,
self.paths.mutation_table_folder, self.paths.database_folder,
self.paths.manual_TSS_folder, self.paths.manual_pro_folder,
self.paths.read_folder, self.paths.bam_folder,
self.paths.target_folder, self.paths.ratt_folder,
self.paths.tsspredator_folder, self.paths.utr_folder,
self.paths.transterm_folder, self.paths.transcript_output_folder,
self.paths.processing_site_folder, self.paths.srna_folder,
self.paths.sorf_folder, self.paths.promoter_output_folder,
self.paths.operon_output_folder, self.paths.circrna_output_folder,
self.paths.goterm_output_folder, self.paths.starget_output_folder,
self.paths.snp_output_folder, self.paths.ppi_output_folder,
self.paths.sublocal_output_folder, self.paths.ribos_output_folder
]
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_set_folder_names(self):
self.paths._set_folder_names()
for folder_name in self.folder_names:
assert (folder_name != '')
self.assertEqual(self.folder_names.count(folder_name), 1)
def test_required_folders(self):
self.assertEqual(len(self.paths.required_folders("root")), 22)
self.assertEqual(len(self.paths.required_folders("get_target_fasta")),
25)
self.assertEqual(len(self.paths.required_folders("TSS")), 27)
self.assertEqual(len(self.paths.required_folders("transcript")), 26)
self.assertEqual(len(self.paths.required_folders("terminator")), 27)
self.assertEqual(
len(self.paths.required_folders("annotation_transfer")), 25)
self.assertEqual(len(self.paths.required_folders("utr")), 29)
self.assertEqual(len(self.paths.required_folders("promoter")), 23)
self.assertEqual(len(self.paths.required_folders("operon")), 26)
self.assertEqual(len(self.paths.required_folders("srna")), 37)
self.assertEqual(len(self.paths.required_folders("sorf")), 30)
self.assertEqual(len(self.paths.required_folders("processing")), 27)
self.assertEqual(len(self.paths.required_folders("riboswitch")), 27)
self.assertEqual(len(self.paths.required_folders("go_term")), 29)
self.assertEqual(len(self.paths.required_folders("ppi_network")), 26)
self.assertEqual(len(self.paths.required_folders("circrna")), 28)
self.assertEqual(len(self.paths.required_folders("crispr")), 26)
self.assertEqual(len(self.paths.required_folders("thermometer")), 27)
self.assertEqual(len(self.paths.required_folders("snp")), 39)
self.assertEqual(
len(self.paths.required_folders("subcellular_localization")), 29)
self.assertEqual(len(self.paths.required_folders("srna_target")), 28)
class Controller(object):
"""Manage the actions of the subcommands.
The Controller take care of providing the argumentes like path
names and the parallel processing of tasks.
"""
def __init__(self, args):
"""Create an instance."""
self._args = args
if (len(args.__dict__) > 3):
if not os.path.exists(args.project_path):
print("Error: --project_path does not exists!")
sys.exit()
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
def check_folder(self, folders, flags):
'''Check the emtpy or wrong assigned folder'''
for folder, flag in zip(folders, flags):
if folder is None:
print("Error: {0} is wrong. Please check it!".format(flag))
sys.exit()
else:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: {0} is a empty folder!".format(flag))
sys.exit()
else:
print("Error: {0} is wrong. Please check it!".format(
flag))
sys.exit()
def check_multi_files(self, input_files, flags):
if input_files is not None:
for files, flag in zip(input_files, flags):
if files is not None:
for file_ in files:
if not os.path.exists(file_):
print("Error: Some files in {0} do "
"not exist!".format(flag))
sys.exit()
def check_parameter(self, paras, names):
'''Check the parameter is assigned correct or not'''
for i in range(len(paras)):
if paras[i] is None:
print("Error: {0} is wrong. "
"Please check it!".format(names[i]))
sys.exit()
def check_no_require_folder(self, folders):
'''Check the folders which are not necessary.
It should not be assigned a empty or wrong folder'''
for folder in folders:
if folder is not None:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: There is a empty folder. "
"Please check it!")
sys.exit()
else:
print("Error: There is a wrong folder. "
"Please check it!")
sys.exit()
def check_execute_file(self, exe):
detect = False
if os.path.exists(exe):
detect = True
full_exe = os.path.realpath(exe)
for folder in os.environ["PATH"].split(":"):
if os.path.exists(os.path.join(folder, exe)):
detect = True
full_exe = exe
if not detect:
if os.path.exists(os.path.realpath(exe)):
full_exe = os.path.realpath(exe)
else:
print("Error: {0} can't be found!".format(exe))
print("Please assign the correct path!")
sys.exit()
return full_exe
def check_file(self, files, names, require):
'''Check the path of file'''
for i in range(len(files)):
if require:
if files[i] is None:
print("Error: {0} is wrong. "
"Please check it!".format(names[i]))
sys.exit()
else:
if not os.path.isfile(files[i]):
print("Error: There is a wrong path of {0}. "
"Please check it!".format(names[i]))
sys.exit()
else:
if files[i] is not None:
if not os.path.isfile(files[i]):
print("Error: There is a wrong path of {0}. "
"Please check it!".format(names[i]))
sys.exit()
def create_project(self, version):
"""Create a new project."""
project_creator.create_root_folder(self._args.project_path)
project_creator.create_subfolders(self._paths.required_folders("root"))
project_creator.create_version_file(
self._paths.version_path, version)
sys.stdout.write("Created folder \"%s\" and required subfolders.\n" % (
self._args.project_path))
def get_input(self):
"""Download required files from website."""
print("Running get input files")
if self._args.ftp_path is None:
print("Error: Please assign the path for downloading the data!")
sys.exit()
annotation_folder = self._paths.ref_annotation_folder
fasta_folder = self._paths.ref_fasta_folder
self.helper.check_make_folder(self._paths.ref_annotation_folder)
self.helper.check_make_folder(self._paths.ref_fasta_folder)
if self._args.ref_gff is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gff")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"_genomic.gff.gz")
if self._args.ref_fasta is True:
get_file(self._args.ftp_path, self._paths.ref_fasta_folder,
"fna")
get_file(self._args.ftp_path, self._paths.ref_fasta_folder,
"_genomic.fna.gz")
if self._args.ref_gbk is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gbk")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"gbff")
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"_genomic.gbff.gz")
if self._args.ref_ptt is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"ptt")
if self._args.ref_rnt is True:
get_file(self._args.ftp_path, self._paths.ref_annotation_folder,
"rnt")
if self._args.convert_embl is True:
annotation_files = os.listdir(self._paths.ref_annotation_folder)
if len(annotation_files) == 0:
sys.stdout.write("No gff files!!\n")
else:
Converter().convert_gbk2embl(self._paths.ref_annotation_folder)
def get_target_fasta(self):
"""Get target fasta"""
print("Running update genome fasta")
self.check_multi_files([self._args.related_fasta_files],
["--related_fasta_files"])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.related_fasta_files)
target.get_target_fasta(
self._args.mutation_table, self._paths.tar_fasta_folder,
self._args.related_fasta_files, self._args.combine_to_one_fasta,
self._paths.target_base_folder)
def ratt(self):
"""Run RATT to transfer annotation file from reference to target."""
print("Running annotation transfer")
if (self._args.transfer_type != "Strain") and (
self._args.transfer_type != "Assembly") and (
self._args.transfer_type != "Species") and (
self._args.transfer_type != "Assembly.Repetitive") and (
self._args.transfer_type != "Strain.Repetitive") and (
self._args.transfer_type != "Species.Repetitive") and (
self._args.transfer_type != "Multiple") and (
self._args.transfer_type != "Free"):
print("Error: please assign correct --transfer_type!")
sys.exit()
if (self._args.related_embl_files is None) and (
self._args.related_gbk_files is None):
print("Error: please assign proper embl or genbank files")
sys.exit()
elif (self._args.related_embl_files is not None) and (
self._args.related_gbk_files is not None):
print("Error: please choose embl as input or genbank as input")
sys.exit()
self._args.ratt_path = self.check_execute_file(self._args.ratt_path)
self.check_multi_files(
[self._args.target_fasta_files, self._args.related_fasta_files],
["--target_fasta_files", "--closed_fasta_files"])
self.check_parameter([self._args.element, self._args.compare_pair],
["--element", "--compare_pair"])
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
project_creator.create_subfolders(
self._paths.required_folders("annotation_transfer"))
args_ratt = self.args_container.container_ratt(
self._args.ratt_path, self._args.element, self._args.transfer_type,
self._args.related_embl_files, self._args.related_gbk_files,
self._args.target_fasta_files, self._args.related_fasta_files,
self._paths.ratt_folder, self._args.convert_to_gff_rnt_ptt,
self._paths.tar_annotation_folder, self._args.compare_pair)
ratt = RATT(args_ratt)
ratt.annotation_transfer(args_ratt)
def tsspredator(self):
"""Run TSSpredator for predicting TSS candidates."""
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files,
self._args.compare_overlap_gff, self._args.manual_files,
self._args.compare_transcript_files],
["--fasta_files", "--annotation_files", "--compare_overlap_gff",
"--manual_files","--compare_transcript_files"])
self.check_parameter([self._args.tex_notex_libs, self._args.condition_names],
["--tex_notex_libs", "--condition_names"])
self._args.tsspredator_path = self.check_execute_file(
self._args.tsspredator_path)
if self._args.program.lower() == "tss":
print("Running TSS prediction")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "ps":
print("Running processing site prediction")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error: No such program!")
sys.exit()
args_tss = self.args_container.container_tsspredator(
self._args.tsspredator_path, self._args.program,
self._args.fasta_files, self._args.annotation_files,
self._args.tex_notex_libs, self._args.condition_names,
self._args.height, self._args.height_reduction,
self._args.factor, self._args.factor_reduction,
self._args.base_height, self._args.enrichment_factor,
self._args.processing_factor, self._args.replicate_tex,
out_folder, self._args.validate_gene,
self._args.manual_files, self._args.curated_sequence_length,
self._args.compare_transcript_files, self._args.tolerance,
self._args.utr_length, self._args.cluster,
self._args.re_check_orphan,
self._args.remove_overlap_feature, self._args.compare_overlap_gff,
self._args.remove_low_expression)
tsspredator = TSSpredator(args_tss)
tsspredator.run_tsspredator(args_tss)
def optimize(self):
"""opimize TSSpredator"""
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files,
self._args.manual_files],
["--fasta_files", "--annotation_files", "--manual_files"])
self._args.tsspredator_path = self.check_execute_file(
self._args.tsspredator_path)
self.check_parameter([self._args.tex_notex_libs,
self._args.condition_names],
["--tex_notex_lib",
"--condition_names"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "ps":
print("Running optimization of processing site prediction")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error: No such program!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.tsspredator_path, self._args.fasta_files,
self._args.annotation_files,
self._args.manual_files, out_folder, self._args.max_height,
self._args.max_height_reduction, self._args.max_factor,
self._args.max_factor_reduction, self._args.max_base_height,
self._args.max_enrichment_factor, self._args.max_processing_factor,
self._args.utr_length, self._args.tex_notex_libs,
self._args.condition_names, self._args.cluster,
self._args.curated_sequence_length, self._args.parallels,
self._args.program, self._args.replicate_tex,
self._args.steps)
optimize_tss(args_ops)
def color(self):
"""color the screenshots"""
print("Running png files coloring")
self.check_parameter([self._args.track_number], ["--track_numer"])
self.check_folder([self._args.screenshot_folder], ["--screenshot_folder"])
self._args.imagemagick_covert_path = self.check_execute_file(
self._args.imagemagick_covert_path)
color = ColorPNG()
color.generate_color_png(
self._args.track_number, self._args.screenshot_folder,
self._args.imagemagick_covert_path)
def terminator(self):
"""Run TransTermHP and Gene converaged for detecting terminators"""
print("Running terminator prediction")
if self._args.transterm_path is None:
print("Please assign the path of transterm in TransTermHP.")
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files,
self._args.transcript_files, self._args.srna_files],
["--fasta_files", "--annotation_files",
"--transcript_files", "--srna_files"])
for prop in ("transterm_path", "expterm_path", "rnafold_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.transterm_path, self._args.expterm_path,
self._args.rnafold_path,
self._paths.transterm_folder, self._args.fasta_files,
self._args.annotation_files, self._args.transcript_files,
self._args.srna_files, self._args.decrease,
self._args.highest_coverage, self._args.tolerance_detect_coverage,
self._args.tolerance_within_transcript,
self._args.tolerance_downstream_transcript,
self._args.tolerance_within_gene,
self._args.tolerance_downstream_gene, self._paths.transtermhp_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicate_tex,
self._args.replicate_frag, self._args.table_best,
self._args.min_loop_length, self._args.max_loop_length,
self._args.min_stem_length, self._args.max_stem_length,
self._args.min_u_tail, self._args.miss_rate,
self._args.mutation_u_tail, self._args.keep_multi_term,
self._args.window_size, self._args.window_shift)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
def transcript(self):
"""Run Transcript detection"""
print("Running transcript detection")
self.check_multi_files(
[self._args.annotation_files, self._args.tss_files,
self._args.terminator_files],
["--annotation_files", "--tss_files", "--terminator_files"])
project_creator.create_subfolders(
self._paths.required_folders("transcript"))
args_tran = self.args_container.container_transcript(
self._args.tex_notex, self._args.modify_transcript,
self._args.length, self._args.annotation_files,
self._args.height, self._args.width,
self._args.tolerance, self._args.tolerance_coverage,
self._args.replicate_tex, self._args.replicate_frag,
self._paths.transcript_output_folder,
self._args.tss_files, self._args.tss_tolerance,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.compare_feature_genome, self._args.table_best,
self._args.terminator_files, self._args.terminator_tolerance,
self._args.max_length_distribution)
transcript = TranscriptDetection(args_tran)
transcript.run_transcript(args_tran)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection")
self.check_multi_files(
[self._args.annotation_files, self._args.terminator_files,
self._args.transcript_files, self._args.tss_files],
["--annotation_files", "--terminator_files",
"--transcript_files", "--tss_files"])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.tss_files, self._args.annotation_files,
self._args.transcript_files, self._args.terminator_files,
self._args.terminator_tolerance, self._paths.utr_folder,
self._args.tss_source, self._args.base_5utr,
self._args.utr_length, self._args.base_3utr,
self._args.tolerance_3utr, self._args.tolerance_5utr)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
def _check_filter_input(self, files, info, filters):
if files is None:
print("Error: The {0} has to be provided "
"if \"{1}\" in --filter_info!".format(info, filters))
sys.exit()
def _check_database(self, database, flag, info):
wrong = False
if database is None:
wrong = True
elif not os.path.isfile(database):
if (os.path.isfile(database + ".fa")) or (
os.path.isfile(database + ".fna")) or (
os.path.isfile(database + ".fasta")):
wrong = False
else:
wrong = True
if wrong:
print("Error: {0} is required if {1} is in --filter_info. "
"But the assignment of {0} is empty or wrong. "
"Please check the {0} or remove {1} from "
"--filter_info!".format(flag, info))
sys.exit()
def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction")
self.check_multi_files(
[self._args.annotation_files, self._args.transcript_files,
self._args.fasta_files, self._args.sorf_files,
self._args.terminator_files, self._args.promoter_tables,
self._args.processing_site_files],
["--annotation_files", "--transcript_files",
"--fasta_files", "--sorf_files", "--terminator_files",
"--promoter_tables", "--processing_site_files"])
for info in self._args.filter_info:
if "sec_str" == info:
if not self._args.compute_sec_structures:
print("Error: --compute_sec_structures is not switch on, "
"but sec_str is still in --filter_info.")
sys.exit()
self._check_filter_input(
self._args.fasta_files, "fasta file", "sec_str")
for prop in ("rnafold_path", "relplot_path",
"mountain_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
elif ("blast_nr" == info) or (
"blast_srna"== info):
for prop in ("blastn_path", "blastx_path", "makeblastdb_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
if ("blast_nr" == info):
self._check_database(self._args.nr_database_path,
"--nr_database_path", "blast_nr")
if ("blast_srna" == info):
self._check_database(self._args.srna_database_path,
"--srna_database_path", "blast_srna")
elif "sorf" == info:
self._check_filter_input(
self._args.sorf_files, "sORF", "sorf")
elif "term" == info:
self._check_filter_input(self._args.terminator_files,
"terminator", "term")
elif "promoter" == info:
self._check_filter_input(self._args.promoter_tables,
"Promoter", "promoter")
elif "tss" == info:
self._check_filter_input(self._args.tss_files,
"TSS", "tss")
else:
if "none" != info.lower():
print("Error: Please check the --filter_info, "
"invalid value was assigned!")
sys.exit()
if self._args.utr_derived_srna:
if self._args.tss_files is None:
print("Error: The TSS has to be provided "
"if you want to compute UTR-derived sRNA!")
sys.exit()
if self._args.search_poly_u != 0:
if self._args.fasta_files is None:
print("Error: The fasta files have to be provided "
"if you want to extend 3'end of sRNA by "
"searching poly U tail!")
sys.exit()
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.rnafold_path, self._args.relplot_path,
self._args.mountain_path, self._args.blastn_path,
self._args.blastx_path, self._args.makeblastdb_path,
self._paths.srna_folder, self._args.utr_derived_srna,
self._args.annotation_files, self._args.tss_files,
self._args.transcript_files,
self._args.tss_intergenic_antisense_tolerance,
self._args.tss_5utr_tolerance, self._args.tss_3utr_tolerance,
self._args.tss_intercds_tolerance, self._args.filter_info,
self._args.processing_site_files, self._args.fasta_files,
self._args.mountain_plot, self._args.nr_format,
self._args.srna_format, self._args.srna_database_path,
self._args.nr_database_path, self._args.cutoff_energy,
self._args.parallel_blast,
self._args.min_intergenic_tex_coverage,
self._args.min_intergenic_notex_coverage,
self._args.min_intergenic_fragmented_coverage,
self._args.min_complete_5utr_transcript_coverage,
self._args.min_antisense_tex_coverage,
self._args.min_antisense_notex_coverage,
self._args.min_antisense_fragmented_coverage,
self._args.min_utr_tex_coverage,
self._args.min_utr_notex_coverage,
self._args.min_utr_fragmented_coverage,
self._args.max_length, self._args.min_length,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.replicate_tex, self._args.replicate_frag,
self._args.tex_notex, self._args.blast_e_nr,
self._args.blast_e_srna, self._args.detect_srna_in_cds,
self._args.table_best, self._args.decrease_intergenic_antisense,
self._args.decrease_utr, self._args.tolerance_intergenic_antisense,
self._args.tolerance_utr, self._args.cutoff_nr_hit,
self._args.sorf_files, self._args.overlap_percent_cds,
self._args.terminator_files,
self._args.terminator_tolerance_in_srna,
self._args.terminator_tolerance_out_srna,
self._args.ignore_hypothetical_protein, self._args.tss_source,
self._args.min_all_utr_coverage, self._args.promoter_tables,
self._args.ranking_time_promoter, self._args.promoter_names,
self._args.compute_sec_structures, self._args.search_poly_u,
self._args.min_u_poly_u, self._args.mutation_poly_u)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction")
self.check_multi_files(
[self._args.transcript_files, self._args.annotation_files,
self._args.fasta_files, self._args.srna_files,
self._args.tss_files],
["--transcript_files", "--annotation_files",
"--fasta_files", "--srna_files", "--tss_files"])
project_creator.create_subfolders(
self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.utr_derived_sorf,
self._args.transcript_files,
self._args.annotation_files,
self._args.tss_files, self._args.utr_length,
self._args.min_length, self._args.max_length,
self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage,
self._args.cutoff_3utr_coverage,
self._args.cutoff_intercds_coverage,
self._args.fasta_files, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicate_tex, self._args.replicate_frag,
self._args.table_best, self._args.srna_files,
self._args.start_codon, self._args.stop_codon,
self._args.cutoff_base_coverage, self._args.tolerance_rbs,
self._args.rbs_not_after_tss, self._args.print_all_combination,
self._args.best_no_srna, self._args.best_no_tss,
self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance,
self._args.tolerance_3end, self._args.tolerance_5end)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)
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)
def operon(self):
"""operon detection"""
print("Running operon detection")
self.check_multi_files(
[self._args.tss_files, self._args.annotation_files,
self._args.transcript_files, self._args.utr5_files,
self._args.utr3_files, self._args.terminator_files],
["--tss_files", "--annotation_files",
"--transcript_files", "--utr5_files",
"--utr3_files", "--terminator_files"])
project_creator.create_subfolders(
self._paths.required_folders("operon"))
args_op = self.args_container.container_operon(
self._args.tss_files, self._args.annotation_files,
self._args.transcript_files, self._args.utr5_files,
self._args.utr3_files, self._args.terminator_files,
self._args.tss_tolerance, self._args.terminator_tolerance,
self._args.min_length, self._paths.operon_output_folder,
self._paths.operon_statistics_folder)
operon = OperonDetection(args_op)
operon.run_operon(args_op)
def circrna(self):
"""circRNA detection"""
print("Running circular RNA prediction")
if self._args.read_files:
self._args.segemehl_path = self.check_execute_file(
self._args.segemehl_path)
for prop in ("testrealign_path", "samtools_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files],
["--fasta_files", "--annotation_files"])
project_creator.create_subfolders(
self._paths.required_folders("circrna"))
args_circ = self.args_container.container_circrna(
self._args.parallels, self._args.fasta_files,
self._args.annotation_files, self._args.bam_files,
self._args.read_files, self._paths.circrna_stat_folder,
self._args.support_reads, self._args.segemehl_path,
self._args.testrealign_path, self._args.samtools_path,
self._args.start_ratio, self._args.end_ratio,
self._args.ignore_hypothetical_protein,
self._paths.circrna_output_folder)
circ = CircRNADetection(args_circ)
circ.run_circrna(args_circ)
def goterm(self):
"""Go term discovery"""
print("Running GO term mapping")
self.check_multi_files(
[self._args.annotation_files, self._args.transcript_files],
["--annotation_files", "--transcript_files"])
self.check_file([self._args.uniprot_id, self._args.go_obo,
self._args.goslim_obo],
["--uniprot_id", "--go.obo", "--goslim_obo"], True)
project_creator.create_subfolders(
self._paths.required_folders("go_term"))
args_go = self.args_container.container_goterm(
self._args.annotation_files,
self._paths.goterm_output_folder, self._args.uniprot_id,
self._args.go_obo, self._args.goslim_obo,
self._args.transcript_files)
goterm = GoTermFinding(args_go)
goterm.run_go_term(args_go)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction")
self.check_multi_files(
[self._args.fasta_files, self._args.srna_files,
self._args.annotation_files],
["--fasta_files", "--srna_files",
"--annotation_files"])
if "RNAup" in self._args.program:
self._args.rnaup_path = self.check_execute_file(
self._args.rnaup_path)
if "RNAplex" in self._args.program:
for prop in ("rnaplfold_path", "rnaplex_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
if "IntaRNA" in self._args.program:
self._args.intarna_path = self.check_execute_file(
self._args.intarna_path)
if self._args.mode_intarna is None:
print("Error: --mode_IntaRNA need to be assigned!")
sys.exit()
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.rnaplfold_path, self._args.rnaplex_path,
self._args.rnaup_path, self._args.intarna_path,
self._args.annotation_files,
self._args.fasta_files, self._args.srna_files,
self._args.query_srnas, self._args.program,
self._args.interaction_length,
self._args.window_size_target_rnaplex,
self._args.span_target_rnaplex,
self._args.window_size_srna_rnaplfold,
self._args.span_srna_rnaplfold,
self._args.unstructured_region_rnaplex_target,
self._args.unstructured_region_rnaplex_srna,
self._args.unstructured_region_rnaup,
self._args.energy_threshold_rnaplex,
self._args.duplex_distance_rnaplex, self._args.top,
self._paths.starget_output_folder, self._args.parallels_rnaplex,
self._args.parallels_rnaup, self._args.parallels_intarna,
self._args.continue_rnaup,
self._args.slide_window_size_srna_intarna,
self._args.max_loop_length_srna_intarna,
self._args.slide_window_size_target_intarna,
self._args.max_loop_length_target_intarna,
self._args.mode_intarna, self._args.potential_target_start,
self._args.potential_target_end, self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling")
self.check_multi_files(
[self._args.fasta_files],
["--fasta_files"])
if (self._args.bam_type != "related_genome") and (
self._args.bam_type != "reference_genome"):
print("Error: Please assign \"related_genome\" or"
" \"reference_genome\" to --bam_type!")
sys.exit()
if (self._args.ploidy != "haploid") and (
self._args.ploidy != "diploid"):
print("Error: Please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!")
if (self._args.caller != "c") and (
self._args.caller != "m"):
print("Error: Please assign \"c\" or"
" \"m\" to --caller!")
for prop in ("bcftools_path", "samtools_path"):
setattr(self._args, prop,
self.check_execute_file(getattr(self._args, prop)))
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type,
self._args.program, self._args.fasta_files,
self._args.bam_files,
self._args.quality, self._args.read_depth_range,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy, self._args.rg_tag, self._args.caller,
self._args.filter_tag_info, self._args.dp4_cutoff)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
def ppi(self):
"""PPI network retrieve"""
print("Running protein-protein interaction networks prediction")
self.check_multi_files([self._args.annotation_files],
["--annotation_files"])
self.check_parameter([self._args.query_strains,
self._args.species_string],
["--query_strains", "--species_string"])
project_creator.create_subfolders(
self._paths.required_folders("ppi_network"))
args_ppi = self.args_container.container_ppi(
self._args.annotation_files, self._args.query_strains,
self._args.without_strain_pubmed, self._args.species_string,
self._args.score, self._paths.ppi_output_folder,
self._args.node_size, self._args.query)
ppi = PPINetwork(self._paths.ppi_output_folder)
ppi.retrieve_ppi_network(args_ppi)
def sublocal(self):
"""Subcellular Localization prediction"""
print("Running subcellular localization prediction")
self.check_multi_files(
[self._args.annotation_files, self._args.fasta_files,
self._args.transcript_files],
["--annotation_files", "--fasta_files",
"--transcript_files"])
if (self._args.bacteria_type != "positive") and (
self._args.bacteria_type != "negative"):
print("Error: Please assign \"positive\" or"
" \"negative\" to --bacteria_type!")
sys.exit()
self._args.psortb_path = self.check_execute_file(self._args.psortb_path)
project_creator.create_subfolders(
self._paths.required_folders("subcellular_localization"))
args_sub = self.args_container.container_sublocal(
self._args.psortb_path, self._args.annotation_files,
self._args.fasta_files, self._args.bacteria_type,
self._args.difference_multi,
self._paths.sublocal_output_folder, self._args.transcript_files)
sublocal = SubLocal(args_sub)
sublocal.run_sub_local(args_sub)
def ribos(self):
"""riboswitch and RNA thermometer prediction"""
print("Running riboswitch and RNA thermometer prediction")
self.check_multi_files(
[self._args.annotation_files, self._args.fasta_files,
self._args.tss_files, self._args.transcript_files],
["--annotation_files", "--fasta_files", "--tss_files",
"--transcript_files"])
if (self._args.program == "both"):
self.check_file([self._args.riboswitch_id_file, self._args.rfam_path],
["--riboswitch_id_file", "--rfam_path"], True)
self.check_file([self._args.rna_thermometer_id_file,
self._args.rfam_path],
["--rna_thermometer_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = self._paths.ribos_output_folder
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "thermometer"):
self.check_file([self._args.rna_thermometer_id_file,
self._args.rfam_path],
["--thermometer_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("thermometer"))
ribos_path = None
thermo_path = self._paths.thermo_output_folder
elif (self._args.program == "riboswitch"):
self.check_file([self._args.riboswitch_id_file, self._args.rfam_path],
["--riboswitch_id_file", "--rfam_path"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
ribos_path = self._paths.ribos_output_folder
thermo_path = None
else:
print("Error: Please assign \"thermometer\", \"riboswitch\" "
"or \"both\" in --program!")
sys.exit()
self._args.cmscan_path = self.check_execute_file(self._args.cmscan_path)
self._args.cmpress_path = self.check_execute_file(self._args.cmpress_path)
args_ribo = self.args_container.container_ribos(
self._args.program, self._args.rna_thermometer_id_file,
self._args.cmscan_path, self._args.cmpress_path,
self._args.riboswitch_id_file,
self._args.annotation_files, self._args.fasta_files,
self._args.tss_files, self._args.transcript_files,
self._args.rfam_path, ribos_path,
thermo_path, self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.tolerance,
self._args.tolerance_rbs, self._args.utr_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def crispr(self):
"""CRISPR prediction"""
print("Running CRISPR prediction")
self.check_multi_files(
[self._args.fasta_files, self._args.annotation_files],
["--fasta_files", "--annotation_files"])
self._args.crt_path = self.check_execute_file(self._args.crt_path)
project_creator.create_subfolders(
self._paths.required_folders("crispr"))
args_cris = self.args_container.container_cris(
self._args.fasta_files, self._args.annotation_files,
self._args.crt_path, self._args.window_size,
self._args.min_number_repeats, self._args.min_length_repeat,
self._args.Max_length_repeat, self._args.min_length_spacer,
self._args.Max_length_spacer, self._paths.crispr_output_folder,
self._args.ignore_hypothetical_protein)
cris = Crispr(args_cris)
cris.run_crispr(args_cris)
def merge(self):
"""Merge all features"""
print("Merging all features to one gff file")
merge_folder = os.path.join(self._paths.output_folder,
"merge_all_features")
self.helper.check_make_folder(merge_folder)
other_features = self._args.other_features_files
self.check_file([self._args.transcript_file] + other_features,
["--transcript_file", "--other_features_files"],
False)
self.check_parameter([self._args.output_prefix], ["--output_prefix"])
run_merge(merge_folder, self._args.transcript_file,
self._args.other_features_files,
self._args.terminator_tolerance, self._args.tss_tolerance,
os.path.join(merge_folder, self._args.output_prefix))
def screen(self):
"""generate screenshot"""
print("Running screenshot generation")
self.check_file([self._args.main_gff, self._args.fasta_file],
["--main_gff", "--fasta_file"], True)
if self._args.side_gffs is not None:
for gff in (self._args.side_gffs):
gff = gff.strip()
if not os.path.isfile(gff):
print("Error: The --side_gffs do not exist!")
sys.exit()
if self._args.output_folder is None:
print("Error: Please assign --output_folder!")
sys.exit()
if (self._args.present != "expand") and (
self._args.present != "collapse") and (
self._args.present != "squish"):
print("Error: Please assign \"expand\" or "
"\"collapse\" or \"squish\" to --present!")
sys.exit()
args_sc = self.args_container.container_screen(
self._args.main_gff, self._args.side_gffs,
self._args.fasta_file, self._args.height,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.present, self._args.output_folder)
screen = Screen(args_sc)
screen.screenshot(args_sc)
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
class TestPaths(unittest.TestCase):
def setUp(self):
self.test_folder = "test_folder"
if not os.path.exists(self.test_folder):
os.mkdir(self.test_folder)
self.paths = Paths(base_path=self.test_folder)
self.folder_names = [
self.paths.input_folder,
self.paths.output_folder,
self.paths.reference_input_folder,
self.paths.wig_folder,
self.paths.mutation_table_folder,
self.paths.database_folder,
self.paths.manual_TSS_folder,
self.paths.manual_pro_folder,
self.paths.read_folder,
self.paths.bam_folder,
self.paths.target_folder,
self.paths.ratt_folder,
self.paths.tsspredator_folder,
self.paths.utr_folder,
self.paths.transterm_folder,
self.paths.transcript_assembly_output_folder,
self.paths.processing_site_folder,
self.paths.srna_folder,
self.paths.sorf_folder,
self.paths.promoter_output_folder,
self.paths.operon_output_folder,
self.paths.circrna_output_folder,
self.paths.goterm_output_folder,
self.paths.starget_output_folder,
self.paths.snp_output_folder,
self.paths.ppi_output_folder,
self.paths.sublocal_output_folder,
self.paths.ribos_output_folder]
def tearDown(self):
if os.path.exists(self.test_folder):
shutil.rmtree(self.test_folder)
def test_set_folder_names(self):
self.paths._set_folder_names()
for folder_name in self.folder_names:
assert(folder_name != '')
self.assertEqual(self.folder_names.count(folder_name), 1)
def test_required_folders(self):
self.assertEqual(len(self.paths.required_folders("root")), 21)
self.assertEqual(len(self.paths.required_folders("get_target_fasta")), 24)
self.assertEqual(len(self.paths.required_folders("TSS")), 26)
self.assertEqual(len(self.paths.required_folders("transcript_assembly")), 25)
self.assertEqual(len(self.paths.required_folders("terminator")), 26)
self.assertEqual(len(self.paths.required_folders("annotation_transfer")), 24)
self.assertEqual(len(self.paths.required_folders("utr")), 28)
self.assertEqual(len(self.paths.required_folders("promoter")), 22)
self.assertEqual(len(self.paths.required_folders("operon")), 25)
self.assertEqual(len(self.paths.required_folders("srna")), 36)
self.assertEqual(len(self.paths.required_folders("sorf")), 29)
self.assertEqual(len(self.paths.required_folders("processing")), 26)
self.assertEqual(len(self.paths.required_folders("riboswitch")), 26)
self.assertEqual(len(self.paths.required_folders("go_term")), 28)
self.assertEqual(len(self.paths.required_folders("ppi_network")), 25)
self.assertEqual(len(self.paths.required_folders("circrna")), 27)
self.assertEqual(len(self.paths.required_folders("snp")), 38)
self.assertEqual(len(self.paths.required_folders("subcellular_localization")), 28)
self.assertEqual(len(self.paths.required_folders("srna_target")), 27)
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
class Controller(object):
"""Manage the actions of the subcommands.
The Controller take care of providing the argumentes like path
names and the parallel processing of tasks.
"""
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
def check_folder(self, folders):
for folder in folders:
if folder is None:
print("Error: There is wrong path of folder assigned, "
"please check it!!")
sys.exit()
else:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: There is empty folder, "
"please check it!!")
sys.exit()
else:
print("Error: There is wrong folder, please check it!!")
sys.exit()
def check_parameter(self, paras, names):
for i in range(len(paras)):
if paras[i] is None:
print("Error: {0} is wrong, "
"please check it!!".format(names[i]))
sys.exit()
def check_no_require_folder(self, folders):
for folder in folders:
if folder is not None:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: There is empty folder, "
"please check it!!")
sys.exit()
else:
print("Error: There is wrong folder, "
"please check it!!")
sys.exit()
def check_file(self, files, names, require):
for i in range(len(files)):
if require:
if files[i] is None:
print("Error: {0} is wrong, "
"please check it!!".format(names[i]))
sys.exit()
else:
if not os.path.isfile(files[i]):
print("Error: There is wrong path of {0}, "
"please check it!!".format(names[i]))
sys.exit()
else:
if files[i] is not None:
if not os.path.isfile(files[i]):
print("Error: There is wrong path of {0}, "
"please check it!!".format(names[i]))
sys.exit()
def create_project(self, version):
"""Create a new project."""
project_creator.create_root_folder(self._args.project_path)
project_creator.create_subfolders(self._paths.required_folders("root"))
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
project_creator.create_version_file(
self._paths.version_path, version)
sys.stdout.write("Created folder \"%s\" and required subfolders.\n" % (
self._args.project_path))
def get_input(self):
"""Download required files from website."""
print("Running get input files...")
if self._args.FTP_path is None:
print("Error: Please assign the path for downloading the data!!")
sys.exit()
if self._args.for_target:
annotation_folder = self._paths.tar_annotation_folder
fasta_folder = self._paths.tar_fasta_folder
else:
annotation_folder = self._paths.ref_annotation_folder
fasta_folder = self._paths.ref_fasta_folder
self.helper.check_make_folder(annotation_folder)
self.helper.check_make_folder(fasta_folder)
if self._args.ref_gff is True:
get_file(self._args.FTP_path, annotation_folder,
"gff", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"_genomic.gff.gz", self._args.for_target)
if self._args.ref_fasta is True:
get_file(self._args.FTP_path, fasta_folder,
"fna", self._args.for_target)
get_file(self._args.FTP_path, fasta_folder,
"_genomic.fna.gz", self._args.for_target)
if self._args.ref_gbk is True:
get_file(self._args.FTP_path, annotation_folder,
"gbk", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"gbff", self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"_genomic.gbff.gz", self._args.for_target)
if self._args.ref_ptt is True:
get_file(self._args.FTP_path, annotation_folder,
"ptt", self._args.for_target)
if self._args.ref_rnt is True:
get_file(self._args.FTP_path, annotation_folder,
"rnt", self._args.for_target)
if self._args.convert_embl is True:
annotation_files = os.listdir(annotation_folder)
if len(annotation_files) == 0:
sys.stdout.write("No gbk files!!\n")
else:
Converter().convert_gbk2embl(annotation_folder)
def get_target_fasta(self):
"""Get target fasta"""
print("Running get target fasta...")
self.check_parameter([self._args.output_format], ["--output_format"])
self.check_folder([self._args.ref_fasta_folder])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
outputs = self._args.output_format.split(",")
for output in outputs:
output = output.strip()
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.ref_fasta_folder)
target.get_target_fasta(
self._args.mutation_table, self._paths.tar_fasta_folder,
self._args.ref_fasta_folder, outputs)
def ratt(self):
"""Run RATT to transfer annotation file from reference to target."""
print("Running annotation transfer...")
if (self._args.transfer_type != "Strain") and (
self._args.transfer_type != "Assembly") and (
self._args.transfer_type != "Species") and (
self._args.transfer_type != "Assembly.Repetitive") and (
self._args.transfer_type != "Strain.Repetitive") and (
self._args.transfer_type != "Species.Repetitive") and (
self._args.transfer_type != "Multiple") and (
self._args.transfer_type != "Free"):
print("Error: please assign correct --transfer_type!!")
sys.exit()
self.check_folder([self._args.ref_embl_gbk, self._args.target_fasta,
self._args.ref_fasta])
self.check_parameter([self._args.element, self._args.compare_pair],
["--element", "--compare_pair"])
project_creator.create_subfolders(
self._paths.required_folders("annotation_transfer"))
args_ratt = self.args_container.container_ratt(
self._args.RATT_path, self._args.element, self._args.transfer_type,
self._args.ref_embl_gbk, self._args.target_fasta,
self._args.ref_fasta, self._paths.ratt_folder,
self._args.convert_to_gff_rnt_ptt,
self._paths.tar_annotation_folder, self._args.compare_pair)
ratt = RATT(args_ratt)
ratt.annotation_transfer(args_ratt)
def tsspredator(self):
"""Run TSSpredator for predicting TSS candidates."""
self.check_folder([self._args.fasta_folder,
self._args.annotation_folder,
self._args.wig_folder])
self.check_parameter([self._args.lib, self._args.output_prefix],
["--lib", "--output_prefix"])
self.check_no_require_folder([self._args.compare_transcript_assembly,
self._args.reference_gff_folder])
self.check_file([self._args.merge_manual], ["--merge_manual"], False)
if self._args.compute_program.lower() == "tss":
print("Running TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.compute_program.lower() == "processing_site":
print("Running processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_tss = self.args_container.container_tsspredator(
self._args.TSSpredator_path, self._args.compute_program,
self._args.fasta_folder, self._args.annotation_folder,
self._args.wig_folder, self._args.lib,
self._args.output_prefix,
self._args.height, self._args.height_reduction,
self._args.factor, self._args.factor_reduction,
self._args.base_height, self._args.enrichment_factor,
self._args.processing_factor, self._args.replicate_match,
out_folder, self._args.statistics,
self._args.validate_gene, self._args.merge_manual,
self._args.compare_transcript_assembly, self._args.fuzzy,
self._args.utr_length, self._args.cluster,
self._args.length, self._args.re_check_orphan,
self._args.overlap_feature, self._args.reference_gff_folder,
self._args.remove_low_expression)
tsspredator = TSSpredator(args_tss)
tsspredator.run_tsspredator(args_tss)
def optimize(self):
"""opimize TSSpredator"""
self.check_folder([self._args.wig_folder, self._args.fasta_file,
self._args.annotation_file])
self.check_file([self._args.manual],
["--manual"], True)
self.check_parameter([self._args.strain_name, self._args.lib,
self._args.output_prefix],
["--strain_name", "--lib", "--output_prefix"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "processing_site":
print("Running optimization of processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.TSSpredator_path, self._args.fasta_file,
self._args.annotation_file, self._args.wig_folder,
self._args.manual, out_folder,
self._args.strain_name, self._args.max_height,
self._args.max_height_reduction, self._args.max_factor,
self._args.max_factor_reduction, self._args.max_base_height,
self._args.max_enrichment_factor, self._args.max_processing_factor,
self._args.utr_length, self._args.lib,
self._args.output_prefix, self._args.cluster,
self._args.length, self._args.core,
self._args.program, self._args.replicate_match,
self._args.steps)
optimize_tss(args_ops)
def color(self):
"""color the screenshots"""
print("Running png files coloring...")
self.check_parameter([self._args.track_number], ["--track_numer"])
self.check_folder([self._args.screenshot_folder])
color = ColorPNG()
color.generate_color_png(
self._args.track_number, self._args.screenshot_folder,
self._args.ImageMagick_covert_path)
def terminator(self):
"""Run TransTermHP for detecting terminators."""
print("Running terminator prediction...")
if self._args.TransTermHP_path is None:
print("Please assign the folder where you install TransTermHP.")
self.check_folder([self._args.fasta_folder,
self._args.annotation_folder,
self._args.transcript_folder])
self.check_no_require_folder([self._args.sRNA])
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.TransTermHP_path, self._args.expterm_path,
self._args.RNAfold_path,
self._paths.transterm_folder, self._args.fasta_folder,
self._args.annotation_folder, self._args.transcript_folder,
self._args.sRNA, self._args.statistics,
self._args.tex_wig_folder, self._args.frag_wig_folder,
self._args.decrease, self._args.highest_coverage,
self._args.fuzzy_detect_coverage,
self._args.fuzzy_within_transcript,
self._args.fuzzy_downstream_transcript,
self._args.fuzzy_within_gene,
self._args.fuzzy_downstream_gene, self._paths.transtermhp_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicates_tex,
self._args.replicates_frag, self._args.table_best,
self._args.min_loop_length, self._args.max_loop_length,
self._args.min_stem_length,
self._args.max_stem_length, self._args.min_U_tail_length,
self._args.miss_rate, self._args.range_U_tail)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
def transcript(self):
"""Run Transcriptome assembly."""
print("Running transcript assembly...")
self.check_folder([self._args.annotation_folder])
self.check_no_require_folder([
self._args.compare_TSS, self._args.compare_genome_annotation,
self._args.terminator_folder])
project_creator.create_subfolders(
self._paths.required_folders("transcript_assembly"))
args_tran = self.args_container.container_transcript(
self._args.frag_wig_path, self._args.tex_wig_path,
self._args.tex_notex,
self._args.length, self._args.annotation_folder,
self._args.height, self._args.width,
self._args.tolerance, self._args.tolerance_coverage,
self._args.replicates_tex, self._args.replicates_frag,
self._paths.transcript_assembly_output_folder,
self._args.compare_TSS, self._args.compare_genome_annotation,
self._args.TSS_fuzzy, self._args.Tex_treated_libs,
self._args.fragmented_libs, self._args.compare_feature_genome,
self._args.table_best, self._args.terminator_folder,
self._args.fuzzy_term)
transcript = TranscriptAssembly(args_tran)
transcript.run_transcript_assembly(args_tran)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection...")
self.check_folder([self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.TSS_folder])
self.check_no_require_folder([self._args.terminator_folder])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.terminator_folder,
self._args.terminator_fuzzy, self._paths.utr_folder,
self._args.TSS_source, self._args.base_5UTR,
self._args.UTR_length, self._args.base_3UTR)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction...")
self.check_folder([self._args.annotation_folder,
self._args.transcript_assembly_folder])
self.check_no_require_folder([self._args.fasta_folder,
self._args.sORF,
self._args.terminator_folder])
self.check_file([self._args.promoter_table],
["--promoter_table"], False)
if self._args.UTR_derived_sRNA:
self.check_folder([self._args.TSS_folder,
self._args.processing_site_folder])
else:
self.check_no_require_folder([self._args.TSS_folder,
self._args.processing_site_folder])
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.Vienna_folder, self._args.Vienna_utils,
self._args.blast_plus_folder,
self._args.ps2pdf14_path, self._paths.srna_folder,
self._args.UTR_derived_sRNA, self._args.annotation_folder,
self._args.TSS_folder, self._args.transcript_assembly_folder,
self._args.TSS_intergenic_fuzzy, self._args.TSS_5UTR_fuzzy,
self._args.TSS_3UTR_fuzzy, self._args.TSS_interCDS_fuzzy,
self._args.import_info, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.processing_site_folder,
self._args.fasta_folder, self._args.mountain_plot,
self._args.nr_format, self._args.srna_format,
self._args.sRNA_database_path, self._args.nr_database_path,
self._args.cutoff_energy,
self._args.run_intergenic_TEX_coverage,
self._args.run_intergenic_noTEX_coverage,
self._args.run_intergenic_fragmented_coverage,
self._args.run_antisense_TEX_coverage,
self._args.run_antisense_noTEX_coverage,
self._args.run_antisense_fragmented_coverage,
self._args.intergenic_tolerance,
self._args.run_utr_TEX_coverage,
self._args.run_utr_noTEX_coverage,
self._args.run_utr_fragmented_coverage,
self._args.max_length, self._args.min_length,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.replicates_tex, self._args.replicates_frag,
self._args.tex_notex, self._args.blast_e_nr,
self._args.blast_e_srna, self._args.detect_sRNA_in_CDS,
self._args.table_best, self._args.decrease_intergenic,
self._args.decrease_utr, self._args.fuzzy_intergenic,
self._args.fuzzy_utr, self._args.cutoff_nr_hit,
self._args.sORF, self._args.best_with_all_sRNAhit,
self._args.best_without_sORF_candidate,
self._args.overlap_percent_CDS,
self._args.terminator_folder,
self._args.terminator_fuzzy_in_CDS,
self._args.terminator_fuzzy_out_CDS,
self._args.best_with_terminator,
self._args.ignore_hypothetical_protein, self._args.TSS_source,
self._args.min_utr_coverage, self._args.promoter_table,
self._args.best_with_promoter,
self._args.ranking_time_promoter, self._args.promoter_name)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction...")
self.check_folder([self._args.transcript_assembly_folder,
self._args.annotation_folder,
self._args.fasta_folder])
self.check_no_require_folder([
self._args.sRNA_folder, self._args.TSS_folder])
project_creator.create_subfolders(
self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.UTR_derived_sORF,
self._args.transcript_assembly_folder,
self._args.annotation_folder,
self._args.TSS_folder, self._args.utr_length,
self._args.min_length, self._args.max_length,
self._args.tex_wig_folder, self._args.frag_wig_folder,
self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage,
self._args.cutoff_3utr_coverage,
self._args.cutoff_interCDS_coverage,
self._args.fasta_folder, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicates_tex, self._args.replicates_frag,
self._args.table_best, self._args.sRNA_folder,
self._args.start_codon, self._args.stop_codon,
self._args.cutoff_background, self._args.fuzzy_rbs,
self._args.rbs_not_after_TSS, self._args.print_all_combination,
self._args.best_no_sRNA, self._args.best_no_TSS,
self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)
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 operon(self):
"""operon detection"""
print("Running operon detection...")
self.check_folder([self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_folder,
self._args.UTR5_folder, self._args.UTR3_folder])
self.check_no_require_folder([self._args.term_folder])
project_creator.create_subfolders(
self._paths.required_folders("operon"))
args_op = self.args_container.container_operon(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_folder, self._args.UTR5_folder,
self._args.UTR3_folder, self._args.term_folder,
self._args.TSS_fuzzy, self._args.term_fuzzy,
self._args.min_length, self._args.statistics,
self._paths.operon_output_folder, self._args.combine_gff,
self._paths.operon_statistics_folder)
operon = OperonDetection(args_op)
operon.run_operon(args_op)
def circrna(self):
"""circRNA detection"""
print("Running circular RNA prediction...")
self.check_folder([self._args.fasta_path, self._args.annotation_path])
self.check_no_require_folder([self._args.tex_bam_path,
self._args.fragmented_bam_path])
project_creator.create_subfolders(
self._paths.required_folders("circrna"))
args_circ = self.args_container.container_circrna(
self._args.align, self._args.process, self._args.fasta_path,
self._args.annotation_path, self._args.tex_bam_path,
self._args.fragmented_bam_path,
self._paths.read_folder, self._paths.circrna_stat_folder,
self._args.support_reads,
self._args.segemehl_folder, self._args.samtools_path,
self._args.start_ratio, self._args.end_ratio,
self._args.ignore_hypothetical_protein,
self._paths.circrna_output_folder)
circ = CircRNADetection(args_circ)
circ.run_circrna(args_circ)
def goterm(self):
"""Go term discovery"""
print("Running GO term mapping...")
self.check_folder([self._args.annotation_path])
self.check_no_require_folder([self._args.transcript_path])
self.check_file([self._args.UniProt_id, self._args.go_obo,
self._args.goslim_obo],
["--UniProt_id", "--go.obo", "--goslim_obo"], True)
project_creator.create_subfolders(
self._paths.required_folders("go_term"))
args_go = self.args_container.container_goterm(
self._args.annotation_path,
self._paths.goterm_output_folder, self._args.UniProt_id,
self._args.go_obo, self._args.goslim_obo,
self._args.transcript_path)
goterm = GoTermFinding(args_go)
goterm.run_go_term(args_go)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction...")
self.check_folder([self._args.fasta_path, self._args.sRNA_path,
self._args.annotation_path])
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.Vienna_folder, self._args.annotation_path,
self._args.fasta_path, self._args.sRNA_path,
self._args.query_sRNA, self._args.program,
self._args.interaction_length, self._args.window_size_target,
self._args.span_target, self._args.window_size_srna,
self._args.span_srna,
self._args.unstructured_region_RNAplex_target,
self._args.unstructured_region_RNAplex_srna,
self._args.unstructured_region_RNAup, self._args.energy_threshold,
self._args.duplex_distance, self._args.top,
self._paths.starget_output_folder, self._args.process_rnaplex,
self._args.process_rnaup, self._args.continue_rnaup,
self._args.potential_target_start, self._args.potential_target_end,
self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling...")
self.check_folder([self._args.fasta_path])
if (self._args.bam_type != "target") and (
self._args.bam_type != "reference"):
print("Error: please assign \"target\" or"
" \"reference\" to --bam_type!!")
sys.exit()
if (self._args.ploidy != "haploid") and (
self._args.ploidy != "diploid"):
print("Error: please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!!")
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type,
self._args.program, self._args.fasta_path,
self._args.tex_bam_path, self._args.frag_bam_path,
self._args.quality, self._args.read_depth,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
def ppi(self):
"""PPI network retrieve"""
print("Running protein-protein interaction networks prediction...")
self.check_folder([self._args.gff_path])
self.check_parameter([self._args.proteinID_strains,
self._args.species_STRING],
["--proteinID_strains", "--species_STRING"])
project_creator.create_subfolders(
self._paths.required_folders("ppi_network"))
args_ppi = self.args_container.container_ppi(
self._args.gff_path, self._args.proteinID_strains,
self._args.without_strain_pubmed, self._args.species_STRING,
self._args.score, self._paths.ppi_output_folder,
self._args.node_size, self._args.query)
ppi = PPINetwork(self._paths.ppi_output_folder)
ppi.retrieve_ppi_network(args_ppi)
def sublocal(self):
"""Subcellular Localization prediction"""
print("Running subcellular localization prediction...")
self.check_folder([self._args.gff_path, self._args.fasta_path])
self.check_no_require_folder([self._args.transcript_path])
if (self._args.bacteria_type != "positive") and (
self._args.bacteria_type != "negative"):
print("Error: please assign \"positive\" or"
" \"negative\" to --bacteria_type!!")
sys.exit()
project_creator.create_subfolders(
self._paths.required_folders("subcellular_localization"))
args_sub = self.args_container.container_sublocal(
self._args.Psortb_path, self._args.gff_path,
self._args.fasta_path, self._args.bacteria_type,
self._args.difference_multi, self._args.merge_to_gff,
self._paths.sublocal_output_folder, self._args.transcript_path)
sublocal = SubLocal(args_sub)
sublocal.run_sub_local(args_sub)
def ribos(self):
"""riboswitch prediction"""
print("Running riboswitch prediction...")
self.check_folder([self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path])
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
args_ribo = self.args_container.container_ribos(
self._args.infernal_path, self._args.riboswitch_ID,
self._args.gff_path, self._args.fasta_path,
self._args.tss_path, self._args.transcript_path,
self._args.Rfam, self._paths.ribos_output_folder,
self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.fuzzy, self._args.start_codon,
self._args.min_dist_rbs, self._args.max_dist_rbs,
self._args.fuzzy_rbs, self._args.UTR_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def screen(self):
"""generate screenshot"""
print("Running screenshot generating...")
self.check_file([self._args.main_gff, self._args.fasta],
["--main_gff", "--fasta"], True)
if self._args.side_gffs is not None:
for gff in (self._args.side_gffs.split(",")):
gff = gff.strip()
if not os.path.isfile(gff):
print("Error: The --side_gffs no exist!!")
sys.exit()
if self._args.output_folder is None:
print("Error: please assign --output_folder!!")
sys.exit()
if (self._args.present != "expand") and (
self._args.present != "collapse") and (
self._args.present != "squish"):
print("Error: please assign \"expand\" or "
"\"collapse\" or \"squish\" to --present!!")
sys.exit()
args_sc = self.args_container.container_screen(
self._args.main_gff, self._args.side_gffs,
self._args.fasta, self._args.frag_wig_folder,
self._args.tex_wig_folder, self._args.height,
self._args.tex_libs, self._args.frag_libs,
self._args.present, self._args.output_folder)
screen = Screen(args_sc)
screen.screenshot(args_sc)
class Controller(object):
"""Manage the actions of the subcommands.
The Controller take care of providing the argumentes like path
names and the parallel processing of tasks.
"""
def __init__(self, args):
"""Create an instance."""
self._args = args
self._paths = Paths(args.project_path)
self.args_container = ArgsContainer()
self.helper = Helper()
def check_folder(self, folders):
for folder in folders:
if folder is None:
print("Error: There is wrong path of folder assigned, "
"please check it!!")
sys.exit()
else:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: There is empty folder, "
"please check it!!")
sys.exit()
else:
print("Error: There is wrong folder, please check it!!")
sys.exit()
def check_parameter(self, paras, names):
for i in range(len(paras)):
if paras[i] is None:
print("Error: {0} is wrong, "
"please check it!!".format(names[i]))
sys.exit()
def check_no_require_folder(self, folders):
for folder in folders:
if folder is not None:
if os.path.exists(folder):
if len(os.listdir(folder)) == 0:
print("Error: There is empty folder, "
"please check it!!")
sys.exit()
else:
print("Error: There is wrong folder, " "please check it!!")
sys.exit()
def check_file(self, files, names, require):
for i in range(len(files)):
if require:
if files[i] is None:
print("Error: {0} is wrong, "
"please check it!!".format(names[i]))
sys.exit()
else:
if not os.path.isfile(files[i]):
print("Error: There is wrong path of {0}, "
"please check it!!".format(names[i]))
sys.exit()
else:
if files[i] is not None:
if not os.path.isfile(files[i]):
print("Error: There is wrong path of {0}, "
"please check it!!".format(names[i]))
sys.exit()
def create_project(self, version):
"""Create a new project."""
project_creator.create_root_folder(self._args.project_path)
project_creator.create_subfolders(self._paths.required_folders("root"))
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
project_creator.create_version_file(self._paths.version_path, version)
sys.stdout.write("Created folder \"%s\" and required subfolders.\n" %
(self._args.project_path))
def get_input(self):
"""Download required files from website."""
print("Running get input files...")
if self._args.FTP_path is None:
print("Error: Please assign the path for downloading the data!!")
sys.exit()
if self._args.for_target:
annotation_folder = self._paths.tar_annotation_folder
fasta_folder = self._paths.tar_fasta_folder
else:
annotation_folder = self._paths.ref_annotation_folder
fasta_folder = self._paths.ref_fasta_folder
self.helper.check_make_folder(annotation_folder)
self.helper.check_make_folder(fasta_folder)
if self._args.ref_gff is True:
get_file(self._args.FTP_path, annotation_folder, "gff",
self._args.for_target)
get_file(self._args.FTP_path, annotation_folder, "_genomic.gff.gz",
self._args.for_target)
if self._args.ref_fasta is True:
get_file(self._args.FTP_path, fasta_folder, "fna",
self._args.for_target)
get_file(self._args.FTP_path, fasta_folder, "_genomic.fna.gz",
self._args.for_target)
if self._args.ref_gbk is True:
get_file(self._args.FTP_path, annotation_folder, "gbk",
self._args.for_target)
get_file(self._args.FTP_path, annotation_folder, "gbff",
self._args.for_target)
get_file(self._args.FTP_path, annotation_folder,
"_genomic.gbff.gz", self._args.for_target)
if self._args.ref_ptt is True:
get_file(self._args.FTP_path, annotation_folder, "ptt",
self._args.for_target)
if self._args.ref_rnt is True:
get_file(self._args.FTP_path, annotation_folder, "rnt",
self._args.for_target)
if self._args.convert_embl is True:
annotation_files = os.listdir(annotation_folder)
if len(annotation_files) == 0:
sys.stdout.write("No gbk files!!\n")
else:
Converter().convert_gbk2embl(annotation_folder)
def get_target_fasta(self):
"""Get target fasta"""
print("Running get target fasta...")
self.check_parameter([self._args.output_format], ["--output_format"])
self.check_folder([self._args.ref_fasta_folder])
self.check_file([self._args.mutation_table], "--mutation_table", True)
project_creator.create_subfolders(
self._paths.required_folders("get_target_fasta"))
outputs = self._args.output_format.split(",")
for output in outputs:
output = output.strip()
target = TargetFasta(self._paths.tar_fasta_folder,
self._args.ref_fasta_folder)
target.get_target_fasta(self._args.mutation_table,
self._paths.tar_fasta_folder,
self._args.ref_fasta_folder, outputs)
def ratt(self):
"""Run RATT to transfer annotation file from reference to target."""
print("Running annotation transfer...")
if (self._args.transfer_type != "Strain") and (
self._args.transfer_type !=
"Assembly") and (self._args.transfer_type != "Species") and (
self._args.transfer_type != "Assembly.Repetitive"
) and (self._args.transfer_type != "Strain.Repetitive") and (
self._args.transfer_type != "Species.Repetitive") and (
self._args.transfer_type !=
"Multiple") and (self._args.transfer_type != "Free"):
print("Error: please assign correct --transfer_type!!")
sys.exit()
self.check_folder([
self._args.ref_embl_gbk, self._args.target_fasta,
self._args.ref_fasta
])
self.check_parameter([self._args.element, self._args.compare_pair],
["--element", "--compare_pair"])
project_creator.create_subfolders(
self._paths.required_folders("annotation_transfer"))
args_ratt = self.args_container.container_ratt(
self._args.RATT_path, self._args.element, self._args.transfer_type,
self._args.ref_embl_gbk, self._args.target_fasta,
self._args.ref_fasta, self._paths.ratt_folder,
self._args.convert_to_gff_rnt_ptt,
self._paths.tar_annotation_folder, self._args.compare_pair)
ratt = RATT(args_ratt)
ratt.annotation_transfer(args_ratt)
def tsspredator(self):
"""Run TSSpredator for predicting TSS candidates."""
self.check_folder([
self._args.fasta_folder, self._args.annotation_folder,
self._args.wig_folder
])
self.check_parameter([self._args.lib, self._args.output_prefix],
["--lib", "--output_prefix"])
self.check_no_require_folder([
self._args.compare_transcript_assembly,
self._args.reference_gff_folder
])
self.check_file([self._args.merge_manual], ["--merge_manual"], False)
if self._args.compute_program.lower() == "tss":
print("Running TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.compute_program.lower() == "processing_site":
print("Running processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_tss = self.args_container.container_tsspredator(
self._args.TSSpredator_path, self._args.compute_program,
self._args.fasta_folder, self._args.annotation_folder,
self._args.wig_folder, self._args.lib, self._args.output_prefix,
self._args.height, self._args.height_reduction, self._args.factor,
self._args.factor_reduction, self._args.base_height,
self._args.enrichment_factor, self._args.processing_factor,
self._args.replicate_match, out_folder, self._args.statistics,
self._args.validate_gene, self._args.merge_manual,
self._args.compare_transcript_assembly, self._args.fuzzy,
self._args.utr_length, self._args.cluster, self._args.length,
self._args.re_check_orphan, self._args.overlap_feature,
self._args.reference_gff_folder, self._args.remove_low_expression)
tsspredator = TSSpredator(args_tss)
tsspredator.run_tsspredator(args_tss)
def optimize(self):
"""opimize TSSpredator"""
self.check_folder([
self._args.wig_folder, self._args.fasta_file,
self._args.annotation_file
])
self.check_file([self._args.manual], ["--manual"], True)
self.check_parameter(
[self._args.strain_name, self._args.lib, self._args.output_prefix],
["--strain_name", "--lib", "--output_prefix"])
if self._args.program.lower() == "tss":
print("Running optimization of TSS prediction...")
project_creator.create_subfolders(
self._paths.required_folders("TSS"))
out_folder = self._paths.tsspredator_folder
elif self._args.program.lower() == "processing_site":
print("Running optimization of processing site prediction...")
out_folder = self._paths.processing_site_folder
project_creator.create_subfolders(
self._paths.required_folders("processing"))
else:
print("Error:No such program!!!!")
sys.exit()
args_ops = self.args_container.container_optimize(
self._args.TSSpredator_path, self._args.fasta_file,
self._args.annotation_file, self._args.wig_folder,
self._args.manual, out_folder, self._args.strain_name,
self._args.max_height, self._args.max_height_reduction,
self._args.max_factor, self._args.max_factor_reduction,
self._args.max_base_height, self._args.max_enrichment_factor,
self._args.max_processing_factor, self._args.utr_length,
self._args.lib, self._args.output_prefix, self._args.cluster,
self._args.length, self._args.core, self._args.program,
self._args.replicate_match, self._args.steps)
optimize_tss(args_ops)
def color(self):
"""color the screenshots"""
print("Running png files coloring...")
self.check_parameter([self._args.track_number], ["--track_numer"])
self.check_folder([self._args.screenshot_folder])
color = ColorPNG()
color.generate_color_png(self._args.track_number,
self._args.screenshot_folder,
self._args.ImageMagick_covert_path)
def terminator(self):
"""Run TransTermHP for detecting terminators."""
print("Running terminator prediction...")
if self._args.TransTermHP_path is None:
print("Please assign the folder where you install TransTermHP.")
self.check_folder([
self._args.fasta_folder, self._args.annotation_folder,
self._args.transcript_folder
])
self.check_no_require_folder([self._args.sRNA])
project_creator.create_subfolders(
self._paths.required_folders("terminator"))
args_term = self.args_container.container_terminator(
self._args.TransTermHP_path, self._args.expterm_path,
self._args.RNAfold_path, self._paths.transterm_folder,
self._args.fasta_folder, self._args.annotation_folder,
self._args.transcript_folder, self._args.sRNA,
self._args.statistics, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.decrease,
self._args.highest_coverage, self._args.fuzzy_detect_coverage,
self._args.fuzzy_within_transcript,
self._args.fuzzy_downstream_transcript,
self._args.fuzzy_within_gene, self._args.fuzzy_downstream_gene,
self._paths.transtermhp_folder, self._args.tex_notex_libs,
self._args.frag_libs, self._args.tex_notex,
self._args.replicates_tex, self._args.replicates_frag,
self._args.table_best, self._args.min_loop_length,
self._args.max_loop_length, self._args.min_stem_length,
self._args.max_stem_length, self._args.min_U_tail_length,
self._args.miss_rate, self._args.range_U_tail)
terminator = Terminator(args_term)
terminator.run_terminator(args_term)
def transcript(self):
"""Run Transcriptome assembly."""
print("Running transcript assembly...")
self.check_folder([self._args.annotation_folder])
self.check_no_require_folder([
self._args.compare_TSS, self._args.compare_genome_annotation,
self._args.terminator_folder
])
project_creator.create_subfolders(
self._paths.required_folders("transcript_assembly"))
args_tran = self.args_container.container_transcript(
self._args.frag_wig_path, self._args.tex_wig_path,
self._args.tex_notex, self._args.length,
self._args.annotation_folder, self._args.height, self._args.width,
self._args.tolerance, self._args.tolerance_coverage,
self._args.replicates_tex, self._args.replicates_frag,
self._paths.transcript_assembly_output_folder,
self._args.compare_TSS, self._args.compare_genome_annotation,
self._args.TSS_fuzzy, self._args.Tex_treated_libs,
self._args.fragmented_libs, self._args.compare_feature_genome,
self._args.table_best, self._args.terminator_folder,
self._args.fuzzy_term)
transcript = TranscriptAssembly(args_tran)
transcript.run_transcript_assembly(args_tran)
def utr_detection(self):
"""Run UTR detection."""
print("Running UTR detection...")
self.check_folder([
self._args.annotation_folder,
self._args.transcript_assembly_folder, self._args.TSS_folder
])
self.check_no_require_folder([self._args.terminator_folder])
project_creator.create_subfolders(self._paths.required_folders("utr"))
args_utr = self.args_container.container_utr(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_assembly_folder,
self._args.terminator_folder, self._args.terminator_fuzzy,
self._paths.utr_folder, self._args.TSS_source,
self._args.base_5UTR, self._args.UTR_length, self._args.base_3UTR)
utr = UTRDetection(args_utr)
utr.run_utr_detection(args_utr)
def srna_detection(self):
"""sRNA_detection."""
print("Running sRNA prediction...")
self.check_folder([
self._args.annotation_folder, self._args.transcript_assembly_folder
])
self.check_no_require_folder([
self._args.fasta_folder, self._args.sORF,
self._args.terminator_folder
])
self.check_file([self._args.promoter_table], ["--promoter_table"],
False)
if self._args.UTR_derived_sRNA:
self.check_folder(
[self._args.TSS_folder, self._args.processing_site_folder])
else:
self.check_no_require_folder(
[self._args.TSS_folder, self._args.processing_site_folder])
project_creator.create_subfolders(self._paths.required_folders("srna"))
args_srna = self.args_container.container_srna(
self._args.Vienna_folder, self._args.Vienna_utils,
self._args.blast_plus_folder, self._args.ps2pdf14_path,
self._paths.srna_folder, self._args.UTR_derived_sRNA,
self._args.annotation_folder, self._args.TSS_folder,
self._args.transcript_assembly_folder,
self._args.TSS_intergenic_fuzzy, self._args.TSS_5UTR_fuzzy,
self._args.TSS_3UTR_fuzzy, self._args.TSS_interCDS_fuzzy,
self._args.import_info, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.processing_site_folder,
self._args.fasta_folder, self._args.mountain_plot,
self._args.nr_format, self._args.srna_format,
self._args.sRNA_database_path, self._args.nr_database_path,
self._args.cutoff_energy, self._args.run_intergenic_TEX_coverage,
self._args.run_intergenic_noTEX_coverage,
self._args.run_intergenic_fragmented_coverage,
self._args.run_antisense_TEX_coverage,
self._args.run_antisense_noTEX_coverage,
self._args.run_antisense_fragmented_coverage,
self._args.intergenic_tolerance, self._args.run_utr_TEX_coverage,
self._args.run_utr_noTEX_coverage,
self._args.run_utr_fragmented_coverage, self._args.max_length,
self._args.min_length, self._args.tex_notex_libs,
self._args.frag_libs, self._args.replicates_tex,
self._args.replicates_frag, self._args.tex_notex,
self._args.blast_e_nr, self._args.blast_e_srna,
self._args.detect_sRNA_in_CDS, self._args.table_best,
self._args.decrease_intergenic, self._args.decrease_utr,
self._args.fuzzy_intergenic, self._args.fuzzy_utr,
self._args.cutoff_nr_hit, self._args.sORF,
self._args.best_with_all_sRNAhit,
self._args.best_without_sORF_candidate,
self._args.overlap_percent_CDS, self._args.terminator_folder,
self._args.terminator_fuzzy_in_CDS,
self._args.terminator_fuzzy_out_CDS,
self._args.best_with_terminator,
self._args.ignore_hypothetical_protein, self._args.TSS_source,
self._args.min_utr_coverage, self._args.promoter_table,
self._args.best_with_promoter, self._args.ranking_time_promoter,
self._args.promoter_name)
srna = sRNADetection(args_srna)
srna.run_srna_detection(args_srna)
def sorf_detection(self):
"""sORF_detection."""
print("Running sORF prediction...")
self.check_folder([
self._args.transcript_assembly_folder,
self._args.annotation_folder, self._args.fasta_folder
])
self.check_no_require_folder(
[self._args.sRNA_folder, self._args.TSS_folder])
project_creator.create_subfolders(self._paths.required_folders("sorf"))
args_sorf = self.args_container.container_sorf(
self._paths.sorf_folder, self._args.UTR_derived_sORF,
self._args.transcript_assembly_folder,
self._args.annotation_folder, self._args.TSS_folder,
self._args.utr_length, self._args.min_length,
self._args.max_length, self._args.tex_wig_folder,
self._args.frag_wig_folder, self._args.cutoff_intergenic_coverage,
self._args.cutoff_antisense_coverage,
self._args.cutoff_5utr_coverage, self._args.cutoff_3utr_coverage,
self._args.cutoff_interCDS_coverage, self._args.fasta_folder,
self._args.tex_notex_libs, self._args.frag_libs,
self._args.tex_notex, self._args.replicates_tex,
self._args.replicates_frag, self._args.table_best,
self._args.sRNA_folder, self._args.start_codon,
self._args.stop_codon, self._args.cutoff_background,
self._args.fuzzy_rbs, self._args.rbs_not_after_TSS,
self._args.print_all_combination, self._args.best_no_sRNA,
self._args.best_no_TSS, self._args.ignore_hypothetical_protein,
self._args.min_rbs_distance, self._args.max_rbs_distance)
sorf = sORFDetection(args_sorf)
sorf.run_sorf_detection(args_sorf)
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 operon(self):
"""operon detection"""
print("Running operon detection...")
self.check_folder([
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_folder, self._args.UTR5_folder,
self._args.UTR3_folder
])
self.check_no_require_folder([self._args.term_folder])
project_creator.create_subfolders(
self._paths.required_folders("operon"))
args_op = self.args_container.container_operon(
self._args.TSS_folder, self._args.annotation_folder,
self._args.transcript_folder, self._args.UTR5_folder,
self._args.UTR3_folder, self._args.term_folder,
self._args.TSS_fuzzy, self._args.term_fuzzy, self._args.min_length,
self._args.statistics, self._paths.operon_output_folder,
self._args.combine_gff, self._paths.operon_statistics_folder)
operon = OperonDetection(args_op)
operon.run_operon(args_op)
def circrna(self):
"""circRNA detection"""
print("Running circular RNA prediction...")
self.check_folder([self._args.fasta_path, self._args.annotation_path])
self.check_no_require_folder(
[self._args.tex_bam_path, self._args.fragmented_bam_path])
project_creator.create_subfolders(
self._paths.required_folders("circrna"))
args_circ = self.args_container.container_circrna(
self._args.align, self._args.process, self._args.fasta_path,
self._args.annotation_path, self._args.tex_bam_path,
self._args.fragmented_bam_path, self._paths.read_folder,
self._paths.circrna_stat_folder, self._args.support_reads,
self._args.segemehl_folder, self._args.samtools_path,
self._args.start_ratio, self._args.end_ratio,
self._args.ignore_hypothetical_protein,
self._paths.circrna_output_folder)
circ = CircRNADetection(args_circ)
circ.run_circrna(args_circ)
def goterm(self):
"""Go term discovery"""
print("Running GO term mapping...")
self.check_folder([self._args.annotation_path])
self.check_no_require_folder([self._args.transcript_path])
self.check_file(
[self._args.UniProt_id, self._args.go_obo, self._args.goslim_obo],
["--UniProt_id", "--go.obo", "--goslim_obo"], True)
project_creator.create_subfolders(
self._paths.required_folders("go_term"))
args_go = self.args_container.container_goterm(
self._args.annotation_path, self._paths.goterm_output_folder,
self._args.UniProt_id, self._args.go_obo, self._args.goslim_obo,
self._args.transcript_path)
goterm = GoTermFinding(args_go)
goterm.run_go_term(args_go)
def srna_target(self):
"""sRNA target prediction"""
print("Running sRNA target prediction...")
self.check_folder([
self._args.fasta_path, self._args.sRNA_path,
self._args.annotation_path
])
project_creator.create_subfolders(
self._paths.required_folders("srna_target"))
args_tar = self.args_container.container_srna_target(
self._args.Vienna_folder, self._args.annotation_path,
self._args.fasta_path, self._args.sRNA_path, self._args.query_sRNA,
self._args.program, self._args.interaction_length,
self._args.window_size_target, self._args.span_target,
self._args.window_size_srna, self._args.span_srna,
self._args.unstructured_region_RNAplex_target,
self._args.unstructured_region_RNAplex_srna,
self._args.unstructured_region_RNAup, self._args.energy_threshold,
self._args.duplex_distance, self._args.top,
self._paths.starget_output_folder, self._args.process_rnaplex,
self._args.process_rnaup, self._args.continue_rnaup,
self._args.potential_target_start, self._args.potential_target_end,
self._args.target_feature)
srnatarget = sRNATargetPrediction(args_tar)
srnatarget.run_srna_target_prediction(args_tar)
def snp(self):
"""SNP transcript detection"""
print("Running SNP/mutations calling...")
self.check_folder([self._args.fasta_path])
if (self._args.bam_type != "target") and (self._args.bam_type !=
"reference"):
print("Error: please assign \"target\" or"
" \"reference\" to --bam_type!!")
sys.exit()
if (self._args.ploidy != "haploid") and (self._args.ploidy !=
"diploid"):
print("Error: please assign \"haploid\" or"
" \"diploid\" to --chromosome_type!!")
project_creator.create_subfolders(self._paths.required_folders("snp"))
args_snp = self.args_container.container_snp(
self._args.samtools_path, self._args.bcftools_path,
self._args.bam_type, self._args.program, self._args.fasta_path,
self._args.tex_bam_path, self._args.frag_bam_path,
self._args.quality, self._args.read_depth,
self._paths.snp_output_folder, self._args.indel_fraction,
self._args.ploidy)
snp = SNPCalling(args_snp)
snp.run_snp_calling(args_snp)
def ppi(self):
"""PPI network retrieve"""
print("Running protein-protein interaction networks prediction...")
self.check_folder([self._args.gff_path])
self.check_parameter(
[self._args.proteinID_strains, self._args.species_STRING],
["--proteinID_strains", "--species_STRING"])
project_creator.create_subfolders(
self._paths.required_folders("ppi_network"))
args_ppi = self.args_container.container_ppi(
self._args.gff_path, self._args.proteinID_strains,
self._args.without_strain_pubmed, self._args.species_STRING,
self._args.score, self._paths.ppi_output_folder,
self._args.node_size, self._args.query)
ppi = PPINetwork(self._paths.ppi_output_folder)
ppi.retrieve_ppi_network(args_ppi)
def sublocal(self):
"""Subcellular Localization prediction"""
print("Running subcellular localization prediction...")
self.check_folder([self._args.gff_path, self._args.fasta_path])
self.check_no_require_folder([self._args.transcript_path])
if (self._args.bacteria_type !=
"positive") and (self._args.bacteria_type != "negative"):
print("Error: please assign \"positive\" or"
" \"negative\" to --bacteria_type!!")
sys.exit()
project_creator.create_subfolders(
self._paths.required_folders("subcellular_localization"))
args_sub = self.args_container.container_sublocal(
self._args.Psortb_path, self._args.gff_path, self._args.fasta_path,
self._args.bacteria_type, self._args.difference_multi,
self._args.merge_to_gff, self._paths.sublocal_output_folder,
self._args.transcript_path)
sublocal = SubLocal(args_sub)
sublocal.run_sub_local(args_sub)
def ribos(self):
"""riboswitch prediction"""
print("Running riboswitch prediction...")
self.check_folder([
self._args.gff_path, self._args.fasta_path, self._args.tss_path,
self._args.transcript_path
])
self.check_file([self._args.riboswitch_ID, self._args.Rfam],
["--riboswitch_ID", "--Rfam"], True)
project_creator.create_subfolders(
self._paths.required_folders("riboswitch"))
args_ribo = self.args_container.container_ribos(
self._args.infernal_path, self._args.riboswitch_ID,
self._args.gff_path, self._args.fasta_path, self._args.tss_path,
self._args.transcript_path, self._args.Rfam,
self._paths.ribos_output_folder, self._args.e_value,
self._args.output_all, self._paths.database_folder,
self._args.fuzzy, self._args.start_codon, self._args.min_dist_rbs,
self._args.max_dist_rbs, self._args.fuzzy_rbs,
self._args.UTR_length)
ribos = Ribos(args_ribo)
ribos.run_ribos(args_ribo)
def screen(self):
"""generate screenshot"""
print("Running screenshot generating...")
self.check_file([self._args.main_gff, self._args.fasta],
["--main_gff", "--fasta"], True)
if self._args.side_gffs is not None:
for gff in (self._args.side_gffs.split(",")):
gff = gff.strip()
if not os.path.isfile(gff):
print("Error: The --side_gffs no exist!!")
sys.exit()
if self._args.output_folder is None:
print("Error: please assign --output_folder!!")
sys.exit()
if (self._args.present != "expand") and (
self._args.present != "collapse") and (self._args.present !=
"squish"):
print("Error: please assign \"expand\" or "
"\"collapse\" or \"squish\" to --present!!")
sys.exit()
args_sc = self.args_container.container_screen(
self._args.main_gff, self._args.side_gffs, self._args.fasta,
self._args.frag_wig_folder, self._args.tex_wig_folder,
self._args.height, self._args.tex_libs, self._args.frag_libs,
self._args.present, self._args.output_folder)
screen = Screen(args_sc)
screen.screenshot(args_sc)