return
if __name__ == '__main__':
# get the path to nr.gz and call main function to download, etc.
# check if nr.gz file path is passed on command line
if len(sys.argv) > 1 and os.path.exists(sys.argv[1]):
selection = sys.argv[1]
# if not, browse to a folder for nr downloads
else:
database = r'C:\Xcalibur\database'
if not os.path.exists(database):
database = os.getcwd()
selection = fasta_lib.get_folder(database,
'Select folder for nr downloads')
if selection == '': sys.exit() # cancel button response
# if folder name starts with 'nr_', then skip creating a new folder
if os.path.split(selection)[1].startswith('nr_'):
main('nr', selection)
# otherwise create a new folder with date stamp
else:
curr_time = time.localtime()
curr_date = '%4d%02d%02d' % (curr_time[0], curr_time[1], curr_time[2])
folder = os.path.join(selection, 'nr_' + curr_date)
if not os.path.exists(folder):
os.mkdir(folder)
main('nr', folder)
def main(taxon_dict):
"""Extracts entries by taxon ID from both Sprot and Trembl databases.
"""
print(
'============================================================================='
)
print(
' uniprot_extract_from_both.py, v.1.1.0, written by Phil Wilmarth, OHSU, 2017 '
)
print(
'============================================================================='
)
# get the UniProt folder and then get the sprot and trembl database names
DB = []
default = r'C:\Xcalibur\database'
if not os.path.exists(default):
default = os.getcwd()
uniprot_folder = fasta_lib.get_folder(
default, title_string='Select a UniProt download folder')
if uniprot_folder == '': sys.exit() # cancel button response
version = uniprot_folder.split('_')[-1]
uniprot_db = 'uniprot'
for files in os.listdir(uniprot_folder):
if files.startswith('uniprot_') and files.endswith('.gz'):
DB.append(os.path.join(uniprot_folder, files))
if len(DB) != 2:
print('WARNING: either sprot or trembl DB was missing')
# create a log file to mirror screen output
log_obj = open(os.path.join(uniprot_folder, 'fasta_utilities.log'), 'a')
write = [None, log_obj]
fasta_lib.time_stamp_logfile(
'\n>>> starting: uniprot_extract_from_both.py', log_obj)
# make the smaller uniprot dictionaries
(sci_to_taxon,
id_to_taxon) = fasta_lib.make_uniprot_to_taxon(uniprot_folder)
# make the more complete dictionary
name_to_taxon = fasta_lib.make_all_names_to_taxon(uniprot_folder)
# print the list of taxon numbers that will be extracted
# NOTE: Any taxon numbers present in analysis text file will not be expanded.
taxon_list = list(taxon_dict.items())
taxon_list.sort()
for obj in write:
print('...extracting these taxon numbers:', file=obj)
for i, t in enumerate(taxon_list):
print('......(%s) taxon %s to file tagged with "%s"' %
(i + 1, t[0], t[1]),
file=obj)
# expand any group taxon numbers
if EXPAND_GROUPS:
fasta_lib.expand_species(uniprot_folder, 'uniprot', taxon_dict,
MIN_SEQUENCE_COUNT, MIN_GROUP_SEQ_COUNT)
# inititalize dictionaries and counters
taxon_files, taxon_count, name_count = {}, {}, {}
for taxon, name in taxon_dict.items():
fname = uniprot_db + '_' + version + '_' + name + '.fasta'
fname = os.path.join(uniprot_folder, fname)
taxon_files[name] = fname
taxon_count[taxon] = 0
name_count[name] = 0
# open the output filenames
for name in taxon_files.keys():
taxon_files[name] = open(taxon_files[name], 'w')
# want to count extracted sequences from each database
name_counter = {}
number_counter = {}
# loop over both databases and extract species
duplicates = {}
for i in range(len(DB)):
prot_read = 0
not_found = 0
for value in taxon_dict.values():
name_counter[value] = 0
for key in taxon_dict.keys():
number_counter[key] = 0
# create a FastaReader object, initialize counters, and start reading
uniprot_file = DB[i]
x = fasta_lib.FastaReader(uniprot_file)
prot = fasta_lib.Protein()
for obj in write:
print('...reading %s and extracting entries...' %
(os.path.split(uniprot_file)[1], ),
file=obj)
# NOTE: checking for errors will slow program execution, use if needed
while x.readNextProtein(prot, check_for_errs=False):
prot_read += 1
if (prot_read % 500000) == 0:
print('......(%s proteins read...)' %
("{0:,d}".format(prot_read), ))
(spec_id,
spec_name) = fasta_lib.uniprot_parse_line(prot.accession + ' ' +
prot.description)
taxon = sci_to_taxon.get(spec_name, 0) # first choice mapping
taxon2 = name_to_taxon.get(spec_name, 0) # alternative mapping
if taxon == 0: # first choice not present
if taxon2 == 0:
not_found += 1
else:
taxon = taxon2 # use second choice
else:
if (taxon != taxon2) and (
taxon2 > 0): # keep track of multiple taxon numbers
duplicates[spec_name] = (taxon, taxon2)
if taxon_dict.get(taxon, False):
if CLEAN_ACCESSIONS:
prot.parseUniProt()
# taxon number matches, so write the protein to respective output file(s)
name = taxon_dict[taxon]
name_counter[name] += 1
name_count[name] += 1
taxon_count[taxon] += 1
number_counter[taxon] += 1
f = taxon_files[name]
prot.printProtein(f)
# print extraction stats for each database
for obj in write:
print('...%s protein entries in %s' %
("{0:,d}".format(prot_read), os.path.split(DB[0])[1]),
file=obj)
print('...%s proteins had unknown taxon numbers' %
("{0:,d}".format(not_found), ),
file=obj)
numbers = list(number_counter.keys())
numbers.sort()
if VERBOSE:
for j, number in enumerate(numbers):
if number_counter[number] > 0:
print('......(%s) taxon %s had %s proteins' %
(j + 1, number, "{0:,d}".format(
number_counter[number])),
file=obj)
names = list(name_counter.keys())
names.sort()
db_name = os.path.split(DB[i])[1]
for j, name in enumerate(names):
print('......(%s) %s %s proteins extracted' %
(j + 1, "{0:,d}".format(name_counter[name]), name),
file=obj)
# close the extracted database files
for f in taxon_files.values():
f.close()
# print list of mis-matched taxon number warnings
if MISMATCHES:
for i, (name, pair) in enumerate(duplicates.items()):
for obj in write:
print('......(%s) WARNING: %s and %s map to "%s"' %
(i + 1, pair[0], pair[1], name),
file=obj)
# print out the final summary stuff
for obj in write:
if VERBOSE:
print('...combined taxon counts...', file=obj)
numbers = list(taxon_count.keys())
numbers.sort()
for i, number in enumerate(numbers):
if taxon_count[number] > 0:
print(
'......(%s) taxon %s had %s proteins' %
(i + 1, number, "{0:,d}".format(taxon_count[number])),
file=obj)
print('...combined output file counts...', file=obj)
for i, name in enumerate(names):
print('......(%s) %s total proteins written to %s' %
(i + 1, "{0:,d}".format(name_count[name]),
uniprot_db + '_' + version + '_' + name + '.fasta'),
file=obj)
fasta_lib.time_stamp_logfile('>>> ending: uniprot_extract_from_both.py',
log_obj)
log_obj.close()
return
species.X_count,
file=obj)
print(" translations that had Z (ambiguous Q/E):",
species.Z_count,
file=obj)
return # attributes added to species should be there after return
# print program name and version
print('===================================================================')
print(' program check_fasta_dir_walk.py, v1.0.0, Phil Wilmarth, OHSU 2020 ')
print('===================================================================')
# select a root folder
root_path = fasta_lib.get_folder(os.getcwd(), 'Select a Root folder')
if not root_path:
sys.exit() # cancel button repsonse
# create a log file to mirror screen output
_folder = root_path
log_obj = open(os.path.join(_folder, 'fasta_utilities.log'), 'a')
write = [None, log_obj]
fasta_lib.time_stamp_logfile('\n>>> starting: check_fasta.py', log_obj)
species_list = []
# process the FASTA files
for root, dirs, files in os.walk(root_path):
for file in files:
if file.endswith(".all.fa.gz"):
species = Species()
def download_databases(self):
"""Fetches the database files for the selected species."""
self.login() # Refresh the FTP connection
# Throw warning if no databases selected
if len(self.tree_right.get_children()) == 0:
messagebox.showwarning("Empty Selection",
"No databases were selected for download!")
return None # Exit function
# Get parent folder location for database download
self.abs_download_path = fasta_lib.get_folder(
self.script_path, 'Select parent folder for database downloads')
if not self.abs_download_path:
return None
# Make a separate folder to contain all files
uniprot_dir_name = r"UniProt_{}".format(self.date)
uniprot_dir_path = os.path.join(self.abs_download_path,
uniprot_dir_name)
try:
os.mkdir(uniprot_dir_path)
except FileExistsError:
pass
os.chdir(uniprot_dir_path)
# Get taxonomy ID numbers for right (download) list
tax_id_list = [
self.tree_right.item(entry)['values'][0]
for entry in self.tree_right.get_children()
]
set_tax_id_list = list(set(tax_id_list)) # remove duplicates (if any)
if len(tax_id_list) != len(set_tax_id_list):
messagebox.showwarning(
"Duplicates found!",
"Duplicate databases were selected and will be ignored!")
# Get the entry objects for the right taxonomy numbers
download_entries = [
entry for entry in self.all_entries
if int(entry.tax_ID) in set_tax_id_list
]
# Add normalized folder name attribute
[entry.make_folder_name(self.date) for entry in download_entries]
for entry in download_entries:
# Move to the FTP site branch where files are located
self.ftp.cwd(entry.ftp_file_path)
# Set local location for the download
download_folder = os.path.join(uniprot_dir_path,
entry.download_folder_name)
try:
os.mkdir(download_folder)
os.chdir(download_folder)
except FileExistsError:
os.chdir(download_folder)
except OSError:
print("OSError")
print('Download for this entry failed:')
entry._snoop()
continue
# Download reference proteome database(s)
for file in entry.ftp_download_list:
# Skip any files that we do not want to download
if self.banned_file(file):
continue
# Download the file (overwrites any existing files)
fixed_file = "{}_{}".format(self.date, file)
self.update_status_bar("Downloading {} file".format(file))
self.ftp.retrbinary('RETR {}'.format(file),
open('{}'.format(file), 'wb').write)
print("{} is done downloading".format(file))
os.rename(os.path.join(download_folder, file),
os.path.join(download_folder, fixed_file))
self.make_fasta_files(uniprot_dir_path, entry)
messagebox.showinfo("All Downloads Completed!", "Downloads Finished!")
self.update_status_bar("Done downloading")
if __name__ == '__main__':
# get path to uniprot databases and call main function to download, etc.
# check if folder path is passed on command line
versions = fasta_lib.get_uniprot_version()
if len(sys.argv) > 1 and os.path.exists(sys.argv[1]):
container = sys.argv[1]
else:
# browse to a container folder for uniprot downloads
# a subfolder will be created with name "uniprot_version"
database = r'C:\Xcalibur\database' # default for BioWorks, XP
if not os.path.exists(database):
database = os.getcwd()
container = fasta_lib.get_folder(
database, 'Select folder for uniprot downloads')
if container == '': sys.exit() # cancel button response
folder = os.path.split(container)[1].lower() # ignore case
if folder.startswith('uniprot_'): # if subfolder, up one level
container = os.path.split(container)[0]
folder = os.path.join(container, 'uniprot_' + versions['uniprot'])
if not os.path.exists(folder): # make folder if necessary
os.mkdir(folder)
# pass in both databases for combined extraction
main(['sprot', 'trembl'], folder, versions)
# end