def print_term(self):
"""
>>> from mimi import mimi_fetch_interactions
>>> from intdb import InteractionDB
>>> test = mimi_fetch_interactions('1436');
>>> db = InteractionDB();
>>> db.add_gene_interactions(test);
>>> db.print_term();
"""
fields = [
'Gene 1',
'Gene 2',
'Components',
'Processes',
'Functions',
'Types',
'Provenance',
'PMIDs'
];
table = PrettyTable(fields);
for f in fields:
table.set_field_align(f,'l');
fracs = [0.05,0.05,0.15,0.15,0.15,0.15,0.15,0.15];
term_width = int(terminal_size()[0]*1.35)
widths = [];
for i in fracs:
widths.append(int(term_width * i));
table.set_field_widths(widths);
gene_root = self.root[InteractionDB._GENE_ROOT];
for uid1 in gene_root:
uid1_root = gene_root.get(uid1);
for uid2 in uid1_root:
inter = uid1_root.get(uid2);
row = [
uid1,
uid2,
["%s [GO:%s]" % (i,j) for i,j in inter.components],
["%s [GO:%s]" % (i,j) for i,j in inter.processes],
["%s [GO:%s]" % (i,j) for i,j in inter.functions],
list(inter.types),
",".join(inter.provenance),
",".join(inter.pmids)
];
table.add_wrapped_row(row);
table.printt(fields=['Gene 1','Gene 2','Types','Provenance','PMIDs']);
table.printt(fields=['Gene 1','Gene 2','Processes','Components','Functions']);
def download(self, logger=None):
if logger is None:
logger = logging.getLogger("pakfire")
downloads = self.get_downloads()
# If there are no downloads, we can just stop here.
if not downloads:
return
# Get free space of the download location.
path = os.path.realpath(REPO_CACHE_DIR)
while not os.path.ismount(path):
path = os.path.dirname(path)
path_stat = os.statvfs(path)
if self.download_size >= path_stat.f_bavail * path_stat.f_bsize:
raise DownloadError, _("Not enough space to download %s of packages.") \
% util.format_size(self.download_size)
logger.info(_("Downloading packages:"))
time_start = time.time()
counter = 0
counter_downloads = len(downloads)
for step in downloads:
counter += 1
# Download the package file.
step.binary_pkg = step.pkg.download(
text="(%d/%d): " % (counter, counter_downloads),
logger=logger)
# Write an empty line to the console when there have been any downloads.
width, height = util.terminal_size()
# Print a nice line.
logger.info("-" * width)
# Format and calculate download information.
time_stop = time.time()
download_time = time_stop - time_start
download_speed = self.download_size / download_time
download_speed = util.format_speed(download_speed)
download_size = util.format_size(self.download_size)
download_time = util.format_time(download_time)
line = "%s | %5sB %s " % \
(download_speed, self.download_size, download_time)
line = " " * (width - len(line)) + line
logger.info(line)
logger.info("")
def download(self, logger=None):
if logger is None:
logger = logging.getLogger("pakfire")
downloads = self.get_downloads()
# If there are no downloads, we can just stop here.
if not downloads:
return
# Get free space of the download location.
path = os.path.realpath(REPO_CACHE_DIR)
while not os.path.ismount(path):
path = os.path.dirname(path)
path_stat = os.statvfs(path)
if self.download_size >= path_stat.f_bavail * path_stat.f_bsize:
raise DownloadError, _("Not enough space to download %s of packages.") \
% util.format_size(self.download_size)
logger.info(_("Downloading packages:"))
time_start = time.time()
counter = 0
counter_downloads = len(downloads)
for step in downloads:
counter += 1
# Download the package file.
step.binary_pkg = step.pkg.download(text="(%d/%d): " %
(counter, counter_downloads),
logger=logger)
# Write an empty line to the console when there have been any downloads.
width, height = util.terminal_size()
# Print a nice line.
logger.info("-" * width)
# Format and calculate download information.
time_stop = time.time()
download_time = time_stop - time_start
download_speed = self.download_size / download_time
download_speed = util.format_speed(download_speed)
download_size = util.format_size(self.download_size)
download_time = util.format_time(download_time)
line = "%s | %5sB %s " % \
(download_speed, self.download_size, download_time)
line = " " * (width - len(line)) + line
logger.info(line)
logger.info("")
def print_term(self):
"""
>>> from mimi import mimi_fetch_interactions
>>> from intdb import InteractionDB
>>> test = mimi_fetch_interactions('1436');
>>> db = InteractionDB();
>>> db.add_gene_interactions(test);
>>> db.print_term();
"""
fields = [
'Gene 1', 'Gene 2', 'Components', 'Processes', 'Functions',
'Types', 'Provenance', 'PMIDs'
]
table = PrettyTable(fields)
for f in fields:
table.set_field_align(f, 'l')
fracs = [0.05, 0.05, 0.15, 0.15, 0.15, 0.15, 0.15, 0.15]
term_width = int(terminal_size()[0] * 1.35)
widths = []
for i in fracs:
widths.append(int(term_width * i))
table.set_field_widths(widths)
gene_root = self.root[InteractionDB._GENE_ROOT]
for uid1 in gene_root:
uid1_root = gene_root.get(uid1)
for uid2 in uid1_root:
inter = uid1_root.get(uid2)
row = [
uid1, uid2,
["%s [GO:%s]" % (i, j) for i, j in inter.components],
["%s [GO:%s]" % (i, j) for i, j in inter.processes],
["%s [GO:%s]" % (i, j) for i, j in inter.functions],
list(inter.types), ",".join(inter.provenance),
",".join(inter.pmids)
]
table.add_wrapped_row(row)
table.printt(
fields=['Gene 1', 'Gene 2', 'Types', 'Provenance', 'PMIDs'])
table.printt(fields=[
'Gene 1', 'Gene 2', 'Processes', 'Components', 'Functions'
])
