def download(self):
self.run.info("Database URL", self.database_url)
for file_name in self.files:
utils.download_file(self.database_url + '/' + file_name,
os.path.join(self.pfam_data_dir, file_name), progress=self.progress, run=self.run)
self.confirm_downloaded_files()
self.decompress_files()
def download(self):
self.run.info("Database URL", self.database_url)
for file_name in self.files:
utils.download_file(self.database_url + '/' + file_name,
os.path.join(self.pfam_data_dir, file_name),
progress=self.progress,
run=self.run)
self.confirm_downloaded_files()
self.decompress_files()
def get_raw_data(self):
if not os.path.exists(self.raw_NCBI_files_dir):
os.mkdir(self.raw_NCBI_files_dir)
open(self.COG_data_dir_version, 'w').write(COG_DATA_VERSION)
for file_name in self.files:
if not 'url' in self.files[file_name]:
continue
file_path = J(self.raw_NCBI_files_dir, file_name)
if not os.path.exists(file_path):
utils.download_file(self.files[file_name]['url'], file_path, progress=progress, run=run)
def download_interacdome_files(self):
"""Download the confident and representable non-redundant InteracDome datasets
These datasets can be found at the interacdome webpage: https://interacdome.princeton.edu/
"""
for path, url in self.interacdome_files.items():
utils.download_file(url,
os.path.join(self.interacdome_data_dir, path),
check_certificate=False,
progress=self.progress,
run=self.run)
def get_raw_data(self):
if not os.path.exists(self.raw_NCBI_files_dir):
os.mkdir(self.raw_NCBI_files_dir)
open(self.COG_data_dir_version, 'w').write(COG_DATA_VERSION)
for file_name in self.files:
if not 'url' in self.files[file_name]:
continue
file_path = J(self.raw_NCBI_files_dir, file_name)
if not os.path.exists(file_path):
utils.download_file(self.files[file_name]['url'], file_path, progress=progress, run=run)
def check_database(self):
"""
Checks for the .bin version of database. If it only finds the .pir version, it binarizes it.
Sets the db filepath.
"""
extensionless, extension = os.path.splitext(self.modeller_database)
if extension not in [".bin", ".pir", ""]:
raise ConfigError(
"MODELLER :: The only possible database extensions are .bin and .pir"
)
bin_db_path = J(self.database_dir, extensionless + ".bin")
pir_db_path = J(self.database_dir, extensionless + ".pir")
bin_exists = utils.filesnpaths.is_file_exists(bin_db_path,
dont_raise=True)
pir_exists = utils.filesnpaths.is_file_exists(pir_db_path,
dont_raise=True)
self.database_path = bin_db_path
if bin_exists:
return
if not pir_exists and not bin_exists:
self.progress.clear()
self.run.warning(
"Anvi'o looked in {} for a database with the name {} and with an extension \
of either .bin or .pir, but didn't find anything matching that \
criteria. Anvi'o will try and download the best database it knows of from \
https://salilab.org/modeller/downloads/pdb_95.pir.gz and use that. \
You can checkout https://salilab.org/modeller/ for more info about the pdb_95 \
database".format(self.database_dir,
self.modeller_database))
db_download_path = os.path.join(self.database_dir, "pdb_95.pir.gz")
utils.download_file(
"https://salilab.org/modeller/downloads/pdb_95.pir.gz",
db_download_path)
utils.run_command(['gzip', '-d', db_download_path],
log_file_path=filesnpaths.get_temp_file_path())
pir_exists = utils.filesnpaths.is_file_exists(pir_db_path,
dont_raise=True)
if pir_exists and not bin_exists:
self.progress.clear()
self.run.warning(
"Your database is not in binary format. That means accessing its contents is slower \
than it could be. Anvi'o is going to make a binary format. Just FYI"
)
self.run_binarize_database(pir_db_path, bin_db_path)
return
def check_database(self):
"""
Checks for the .bin version of database. If it only finds the .pir version, it binarizes it.
Sets the db filepath.
"""
extensionless, extension = os.path.splitext(self.modeller_database)
if extension not in [".bin",".pir",""]:
raise ConfigError("MODELLER :: The only possible database extensions are .bin and .pir")
bin_db_path = J(self.database_dir, extensionless+".bin")
pir_db_path = J(self.database_dir, extensionless+".pir")
bin_exists = utils.filesnpaths.is_file_exists(bin_db_path, dont_raise=True)
pir_exists = utils.filesnpaths.is_file_exists(pir_db_path, dont_raise=True)
self.database_path = bin_db_path
if bin_exists:
return
if not pir_exists and not bin_exists:
self.progress.clear()
self.run.warning("Anvi'o looked in {} for a database with the name {} and with an extension \
of either .bin or .pir, but didn't find anything matching that \
criteria. We'll try and download the best database we know of from \
https://salilab.org/modeller/downloads/pdb_95.pir.gz and use that. \
You can checkout https://salilab.org/modeller/ for more info about the pdb_95 \
database".format(self.database_dir, self.modeller_database))
db_download_path = os.path.join(self.database_dir, "pdb_95.pir.gz")
utils.download_file("https://salilab.org/modeller/downloads/pdb_95.pir.gz", db_download_path)
utils.run_command(['gzip', '-d', db_download_path], log_file_path=filesnpaths.get_temp_file_path())
pir_exists = utils.filesnpaths.is_file_exists(pir_db_path, dont_raise=True)
if pir_exists and not bin_exists:
self.progress.clear()
self.run.warning("Your database is not in binary format. That means accessing its contents is slower \
than it could be. Anvi'o is going to make a binary format. Just FYI")
self.run_binarize_database(pir_db_path, bin_db_path)
return
def check_database(self):
"""Setup the database files
Downloads the .pir file if it is missing
Binarizes .pir file if .bin is missing
Creates the .dmnd file if it is missing
"""
bin_db_path = J(self.database_dir, self.modeller_database + ".bin")
pir_db_path = J(self.database_dir, self.modeller_database + ".pir")
bin_exists = utils.filesnpaths.is_file_exists(bin_db_path,
dont_raise=True)
pir_exists = utils.filesnpaths.is_file_exists(pir_db_path,
dont_raise=True)
if bin_exists and pir_exists:
# We good
pass
else:
if not pir_exists:
# Download .pir
self.run.warning(
"Anvi'o looked in {} for a database with the name {} and with an extension "
"of either .bin or .pir, but didn't find anything matching that "
"criteria. Anvi'o will try and download the best database it knows of from "
"https://salilab.org/modeller/downloads/pdb_95.pir.gz and use that. "
"You can checkout https://salilab.org/modeller/ for more info about the pdb_95 "
"database".format(self.database_dir,
self.modeller_database))
db_download_path = os.path.join(self.database_dir,
"pdb_95.pir.gz")
utils.download_file(
"https://salilab.org/modeller/downloads/pdb_95.pir.gz",
db_download_path)
utils.run_command(
['gzip', '-d', db_download_path],
log_file_path=filesnpaths.get_temp_file_path())
# Binarize .pir (make .bin)
self.run.warning(
"Your database is not in binary format. That means accessing its contents is slower "
"than it could be. Anvi'o is going to make a binary format. Just FYI"
)
self.run_binarize_database(pir_db_path, bin_db_path)
dmnd_db_path = J(self.database_dir, self.modeller_database + '.dmnd')
if os.path.exists(dmnd_db_path):
return
self.run.warning(
"Your diamond database does not exist. It will be created.")
script_name = "pir_to_fasta.py"
self.copy_script_to_directory(script_name)
input_pir_path = J(self.database_dir, self.modeller_database + '.pir')
fasta_path = J(self.database_dir, self.modeller_database + '.fa')
dmnd_path = J(self.database_dir, self.modeller_database)
command = [self.executable, script_name, input_pir_path, fasta_path]
self.run_command(command, script_name=script_name, rename_log=False)
temp = u.FastaOutput(filesnpaths.get_temp_file_path())
fasta = u.SequenceSource(fasta_path)
while next(fasta):
temp.write_id(fasta.id)
temp.write_seq(fasta.seq.replace('-', '').replace('.', 'X'))
shutil.move(temp.output_file_path, fasta_path)
fasta.close()
temp.close()
driver = diamond.Diamond(
query_fasta=fasta_path,
run=terminal.Run(verbose=False),
progress=terminal.Progress(verbose=False),
)
driver.makedb(output_file_path=dmnd_path)
os.remove(fasta_path)
