def download_data(cls, taxid=None, progress_callback=None):
""" Download the data for ``taxid`` from the GeneMANIA
website and initialize the local database.
"""
import tarfile
baseurl = "http://genemania.org/data/current/"
directory = orngServerFiles.localpath("PPI")
if not os.path.exists(directory):
os.makedirs(directory)
if taxid is None:
taxid = cls.common_taxids()
if isinstance(taxid, (list, tuple)):
taxids = taxid
else:
taxids = [taxid]
for taxid in taxids:
name = obiTaxonomy.name(taxid)
name = name.replace(" ", "_")
if progress_callback is None:
progress = True #orngServerFiles.ConsoleProgressBar("Downloading %r." % filename)
else:
progress = progress_callback
filename = name + ".tgz"
url = baseurl + "networks/" + filename
wget(url, directory=directory, progress=progress)
tgz_filename = os.path.join(directory, filename)
tgz = tarfile.open(tgz_filename)
tgz.extractall(directory)
filename = name + ".COMBINED.tgz"
url = baseurl + "precombined/" + filename
wget(url, directory=directory, progress=progress)
tgz_filename = os.path.join(directory, filename)
tgz = tarfile.open(tgz_filename)
tgz.extractall(directory)
cls.init_db([taxid])
def download_data(cls, taxid=None, progress_callback=None):
""" Download the data for ``taxid`` from the GeneMANIA
website and initialize the local database.
"""
import tarfile
baseurl = "http://genemania.org/data/current/"
directory = orngServerFiles.localpath("PPI")
if not os.path.exists(directory):
os.makedirs(directory)
if taxid is None:
taxid = cls.common_taxids()
if isinstance(taxid, (list, tuple)):
taxids = taxid
else:
taxids = [taxid]
for taxid in taxids:
name = obiTaxonomy.name(taxid)
name = name.replace(" ", "_")
if progress_callback is None:
progress = True #orngServerFiles.ConsoleProgressBar("Downloading %r." % filename)
else:
progress = progress_callback
filename = name + ".tgz"
url = baseurl + "networks/" + filename
wget(url, directory=directory, progress=progress)
tgz_filename = os.path.join(directory, filename)
tgz = tarfile.open(tgz_filename)
tgz.extractall(directory)
filename = name + ".COMBINED.tgz"
url = baseurl + "precombined/" + filename
wget(url, directory=directory, progress=progress)
tgz_filename = os.path.join(directory, filename)
tgz = tarfile.open(tgz_filename)
tgz.extractall(directory)
cls.init_db([taxid])
def download(filename, url):
with open(pjoin(cache_dir, filename + ".tmp"), "wb") as dest:
wget(url, dst_obj=dest, progress=True)
shutil.move(pjoin(cache_dir, filename + ".tmp"),
pjoin(cache_dir, filename))
def init_db(cls, version, taxid, cache_dir=None, dbfilename=None):
if cache_dir is None:
cache_dir = serverfiles.localpath(cls.DOMAIN)
if dbfilename is None:
dbfilename = serverfiles.localpath(
cls.DOMAIN,
"string-protein-detailed.{taxid}.sqlite".format(taxid=taxid)
)
pjoin = os.path.join
base_url = "http://string-db.org/newstring_download/"
filename = "{taxid}.protein.links.detailed.{version}.txt.gz"
filename = filename.format(version=version, taxid=taxid)
url = base_url + "protein.links.detailed.{version}/" + filename
url = url.format(version=version)
if not os.path.exists(pjoin(cache_dir, filename)):
wget(url, cache_dir, progress=True)
links_fileobj = open(pjoin(cache_dir, filename), "rb")
links_file = gzip.GzipFile(fileobj=links_fileobj)
con = sqlite3.connect(dbfilename)
with con:
con.execute("""
DROP TABLE IF EXISTS evidence
""")
con.execute("""
CREATE TABLE evidence(
protein_id1 TEXT,
protein_id2 TEXT,
neighborhood INTEGER,
fusion INTEGER,
cooccurence INTEGER,
coexpression INTEGER,
experimental INTEGER,
database INTEGER,
textmining INTEGER
)
""")
links = csv.reader(links_file, delimiter=" ")
links.next() # Read header
filesize = os.stat(pjoin(cache_dir, filename)).st_size
progress = ConsoleProgressBar("Processing links file:")
progress(1.0)
def read_links(reader):
for i, (p1, p2, n, f, c, cx, ex, db, t, _) in \
enumerate(reader):
yield p1, p2, n, f, c, cx, ex, db, t
if i % 10000 == 0:
progress(100.0 * links_fileobj.tell() / filesize)
con.executemany("""
INSERT INTO evidence
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
""", read_links(links))
progress.finish()
print("Indexing")
con.execute("""\
CREATE INDEX IF NOT EXISTS index_evidence
ON evidence (protein_id1, protein_id2)
""")
con.executescript("""
DROP TABLE IF EXISTS version;
CREATE TABLE version (
string_version text,
api_version text
);
""")
con.execute("""
INSERT INTO version
VALUES (?, ?)""", (version, cls.VERSION))
