def fetch_xray(xray_fp, force_download=False):
"""Fetch list of pdb entries, process, and write results to a yaml file.
List of all PDB entries, identification of each as a protein,
nucleic acid, or protein-nucleic acid complex and whether
the structure was determined by diffraction or NMR.
Reference:
http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/summaries.html
Args:
xray_fp (Unicode): The destination yaml file to be written.
force_download (bool): If true, download the file even it
the path already exists locally.
Returns:
None
"""
# Manually unit tested.
if isfile(xray_fp) and not force_download:
print(
"Found local copy of \"{}.\" Using file:\n\t{}".format(
basename(xray_fp),
xray_fp
)
)
return None
assert os.path.isabs(xray_fp)
remote_directory = '/pub/pdb/derived_data/'
remote_file = 'pdb_entry_type.txt'
domain = 'ftp.wwpdb.org'
ftp = FTP(domain)
ftp.login()
ftp.cwd(remote_directory)
lines = []
ftp.retrlines('RETR {}'.format(remote_file), lambda l: lines.append(l))
xray = []
for line in lines:
columns = line.split()
x_type = columns[2].strip()
p_type = columns[1]
pdb = columns[0]
if p_type == 'prot' or p_type == 'prot-nuc':
if x_type == 'diffraction':
xray.append(pdb.upper())
write_yaml(xray, xray_fp)
assert isfile(xray_fp)
return None
def fetch_obsolete(
obs_file_path,
url='http://www.rcsb.org/pdb/rest/getObsolete',
force_download=False
):
"""Fetch list of obsolete entries.
Fetch list of obsolete entries, process, and write
results to a yaml file.
Args:
obs_file_path (Unicode): The destination yaml file to be written.
url (Unicode): The url address of the data.
force_download (bool): If true, download the file even it
the path already exists locally.
Returns:
None
"""
if isfile(obs_file_path) and not force_download:
print(
"Found local copy of \"{}.\" Using file:\n\t{}".format(
basename(obs_file_path),
obs_file_path
)
)
else:
obs = []
obs_req = requests.get(url)
root = ETree.fromstring(obs_req.text)
for child in root:
obs.append(child.attrib['structureId'].upper())
obs_req.close()
write_yaml(obs, obs_file_path)
return None
def uniprot_composite(dirs):
"""Creates final UniProt DataFrame.
Create final UniProt DataFrame where the
UniProt ID provides a unique key.
Args:
dirs (ProjectFolders): A named tuple of directory paths.
"""
pdb_initial_composite_fp = os.path.join(dirs.tsv_data, "pdb_initial_composite_df.tsv")
assert os.path.isfile(pdb_initial_composite_fp)
uni_folder_path = dirs.uni_data
file_names = _create_composite_file_names()
paths = _create_composite_file_paths(uni_folder_path, file_names)
uni_composite_tsv = paths["tsv_file"]
uni_composite_yaml = paths["yaml_file"]
uni_composite_json = paths["json_file"]
if _uni_composite_file_exists(uni_folder_path):
print(
"A final uni_composite file already exists. Composite "
"function complete. (Note: remove existing uni_composite "
'files in the "{}" directory to have them '
"regenerated.".format(uni_folder_path)
)
return None
pdb_df = pd.read_csv(
pdb_initial_composite_fp, sep="\t", header=0, encoding="utf-8", keep_default_na=False, na_values=["NULL", "N/A"]
)
print("Creating the UniProt composite structure.")
uni_df = create_uni_struct(pdb_df)
print("Done creating UniProt composite structure.")
print("Validating UniProt composite structure.")
uni_pdb_validation(uni_df, pdb_df)
print("Validation complete.")
print("Assigning missing region designations.")
uni_df = create_intervals(pdb_df, uni_df)
print("Done assigning missing regions.")
assert isinstance(uni_df, pd.DataFrame)
delimiter = create_delimiter("\t")
uni_df.to_csv(uni_composite_tsv, sep=delimiter, encoding="utf-8")
uni_df.to_json(uni_composite_json, force_ascii=False)
json_data = read_json(uni_composite_json)
write_yaml(json_data, uni_composite_yaml)
print("Done writing UniProt composite files:")
print("\t{}".format(uni_composite_tsv))
print("\t{}".format(uni_composite_yaml))
print("\t{}".format(uni_composite_json))
print("This is the final UniProt ID DataFrame.")
return None