text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
|---|---|
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def cursor(self):
"""The position of the cursor in the text.""" |
if self._cursor < 0:
self.cursor = 0
if self._cursor > len(self):
self.cursor = len(self)
return self._cursor |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def delete_one_letter(self, letter=RIGHT):
"""Delete one letter the right or the the left of the cursor.""" |
assert letter in (self.RIGHT, self.LEFT)
if letter == self.LEFT:
papy = self.cursor
self.text = self.text[:self.cursor - 1] + self.text[self.cursor:]
self.cursor = papy - 1
else:
self.text = self.text[:self.cursor] + self.text[self.cursor + 1:] |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def delete_one_word(self, word=RIGHT):
"""Delete one word the right or the the left of the cursor.""" |
assert word in (self.RIGHT, self.LEFT)
if word == self.RIGHT:
papy = self.text.find(' ', self.cursor) + 1
if not papy:
papy = len(self.text)
self.text = self.text[:self.cursor] + self.text[papy:]
else:
papy = self.text.rfind(' '... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def add_letter(self, letter):
"""Add a letter at the cursor pos.""" |
assert isinstance(letter, str)
assert len(letter) == 1
self.text = self.text[:self.cursor] + letter + self.text[self.cursor:]
self.cursor += 1 |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def update(self, event_or_list):
"""Update the text and position of cursor according to the event passed.""" |
event_or_list = super().update(event_or_list)
for e in event_or_list:
if e.type == KEYDOWN:
if e.key == K_RIGHT:
if e.mod * KMOD_CTRL:
self.move_cursor_one_word(self.RIGHT)
else:
self.m... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def shawn_text(self):
"""The text displayed instead of the real one.""" |
if len(self._shawn_text) == len(self):
return self._shawn_text
if self.style == self.DOTS:
return chr(0x2022) * len(self)
ranges = [
(902, 1366),
(192, 683),
(33, 122)
]
s = ''
while len(s) < len(self.text):... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def cursor_pos(self):
"""The cursor position in pixels.""" |
if len(self) == 0:
return self.left + self.default_text.get_width()
papy = self._surface.get_width()
if papy > self.w:
shift = papy - self.width
else:
shift = 0
return self.left + self.font.size(self.shawn_text[:self.cursor])[0] - shift |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def latex_to_img(tex):
"""Return a pygame image from a latex template.""" |
with tempfile.TemporaryDirectory() as tmpdirname:
with open(tmpdirname + r'\tex.tex', 'w') as f:
f.write(tex)
os.system(r"latex {0}\tex.tex -halt-on-error -interaction=batchmode -disable-installer -aux-directory={0} "
r"-output-directory={0}".forma... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def name2rgb(name):
"""Convert the name of a color into its RGB value""" |
try:
import colour
except ImportError:
raise ImportError('You need colour to be installed: pip install colour')
c = colour.Color(name)
color = int(c.red * 255), int(c.green * 255), int(c.blue * 255)
return color |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_page(page):
"""Parse the command man page.""" |
colors = get_config()['colors']
with io.open(page, encoding='utf-8') as f:
lines = f.readlines()
output_lines = []
for line in lines[1:]:
if is_headline(line):
continue
elif is_description(line):
output_lines.append(click.style(line.replace('>', ' '),
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def configure_logging(level=logging.DEBUG):
"""Configure the module logging engine.""" |
if level == logging.DEBUG:
# For debugging purposes, log from everyone!
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s - %(levelname)s - %(message)s'
)
return logging
logger = logging.getLogger(__name__)
logger.setLevel(level)
form... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_username_password_hostname(remote_url):
""" Parse a command line string and return username, password, remote hostname and remote path. :param remote_u... |
assert remote_url
assert ':' in remote_url
if '@' in remote_url:
username, hostname = remote_url.rsplit('@', 1)
else:
username, hostname = None, remote_url
hostname, remote_path = hostname.split(':', 1)
password = None
if username and ':' in username:
username, pa... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_ssh_agent_keys(logger):
""" Ask the SSH agent for a list of keys, and return it. :return: A reference to the SSH agent and a list of keys. """ |
agent, agent_keys = None, None
try:
agent = paramiko.agent.Agent()
_agent_keys = agent.get_keys()
if not _agent_keys:
agent.close()
logger.error(
"SSH agent didn't provide any valid key. Trying to continue..."
)
else:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def create_parser():
"""Create the CLI argument parser.""" |
parser = argparse.ArgumentParser(
description='Sync a local and a remote folder through SFTP.'
)
parser.add_argument(
"path",
type=str,
metavar="local-path",
help="the path of the local folder",
)
parser.add_argument(
"remote",
type=str,
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def main(args=None):
"""The main.""" |
parser = create_parser()
args = vars(parser.parse_args(args))
log_mapping = {
'CRITICAL': logging.CRITICAL,
'ERROR': logging.ERROR,
'WARNING': logging.WARNING,
'INFO': logging.INFO,
'DEBUG': logging.DEBUG,
'NOTSET': logging.NOTSET,
}
log_level = log_... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def _must_be_deleted(local_path, r_st):
"""Return True if the remote correspondent of local_path has to be deleted. i.e. if it doesn't exists locally or if it ha... |
# if the file doesn't exists
if not os.path.lexists(local_path):
return True
# or if the file type is different
l_st = os.lstat(local_path)
if S_IFMT(r_st.st_mode) != S_IFMT(l_st.st_mode):
return True
return False |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def file_upload(self, local_path, remote_path, l_st):
"""Upload local_path to remote_path and set permission and mtime.""" |
self.sftp.put(local_path, remote_path)
self._match_modes(remote_path, l_st) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def remote_delete(self, remote_path, r_st):
"""Remove the remote directory node.""" |
# If it's a directory, then delete content and directory
if S_ISDIR(r_st.st_mode):
for item in self.sftp.listdir_attr(remote_path):
full_path = path_join(remote_path, item.filename)
self.remote_delete(full_path, item)
self.sftp.rmdir(remote_path)
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def check_for_deletion(self, relative_path=None):
"""Traverse the entire remote_path tree. Find files/directories that need to be deleted, not being present in t... |
if not relative_path:
relative_path = str() # root of shared directory tree
remote_path = path_join(self.remote_path, relative_path)
local_path = path_join(self.local_path, relative_path)
for remote_st in self.sftp.listdir_attr(remote_path):
r_lstat = self.sft... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def create_update_symlink(self, link_destination, remote_path):
"""Create a new link pointing to link_destination in remote_path position.""" |
try: # if there's anything, delete it
self.sftp.remove(remote_path)
except IOError: # that's fine, nothing exists there!
pass
finally: # and recreate the link
try:
self.sftp.symlink(link_destination, remote_path)
except OSError ... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def run(self):
"""Run the sync. Confront the local and the remote directories and perform the needed changes.""" |
# Check if remote path is present
try:
self.sftp.stat(self.remote_path)
except FileNotFoundError as e:
if self.create_remote_directory:
self.sftp.mkdir(self.remote_path)
self.logger.info(
"Created missing remote dir: '... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def list_files(start_path):
"""tree unix command replacement.""" |
s = u'\n'
for root, dirs, files in os.walk(start_path):
level = root.replace(start_path, '').count(os.sep)
indent = ' ' * 4 * level
s += u'{}{}/\n'.format(indent, os.path.basename(root))
sub_indent = ' ' * 4 * (level + 1)
for f in files:
s += u'{}{}\n'.format... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def file_tree(start_path):
""" Create a nested dictionary that represents the folder structure of `start_path`. Liberally adapted from http://code.activestate.co... |
nested_dirs = {}
root_dir = start_path.rstrip(os.sep)
start = root_dir.rfind(os.sep) + 1
for path, dirs, files in os.walk(root_dir):
folders = path[start:].split(os.sep)
subdir = dict.fromkeys(files)
parent = reduce(dict.get, folders[:-1], nested_dirs)
parent[folders[-1]... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def capture_sys_output():
"""Capture standard output and error.""" |
capture_out, capture_err = StringIO(), StringIO()
current_out, current_err = sys.stdout, sys.stderr
try:
sys.stdout, sys.stderr = capture_out, capture_err
yield capture_out, capture_err
finally:
sys.stdout, sys.stderr = current_out, current_err |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def suppress_logging(log_level=logging.CRITICAL):
"""Suppress logging.""" |
logging.disable(log_level)
yield
logging.disable(logging.NOTSET) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def override_env_variables():
"""Override user environmental variables with custom one.""" |
env_vars = ("LOGNAME", "USER", "LNAME", "USERNAME")
old = [os.environ[v] if v in os.environ else None for v in env_vars]
for v in env_vars:
os.environ[v] = "test"
yield
for i, v in enumerate(env_vars):
if old[i]:
os.environ[v] = old[i] |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_config():
"""Get the configurations from .tldrrc and return it as a dict.""" |
config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if not path.exists(config_path):
sys.exit("Can't find config file at: {0}. You may use `tldr init` "
"to init the config file.".format(config_path))
with io.open(config... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_man_page(command, platform):
"""Parse the man page and return the parsed lines.""" |
page_path = find_page_location(command, platform)
output_lines = parse_page(page_path)
return output_lines |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def find_page_location(command, specified_platform):
"""Find the command man page in the pages directory.""" |
repo_directory = get_config()['repo_directory']
default_platform = get_config()['platform']
command_platform = (
specified_platform if specified_platform else default_platform)
with io.open(path.join(repo_directory, 'pages/index.json'),
encoding='utf-8') as f:
index = ... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def find(command, on):
"""Find the command usage.""" |
output_lines = parse_man_page(command, on)
click.echo(''.join(output_lines)) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def update():
"""Update to the latest pages.""" |
repo_directory = get_config()['repo_directory']
os.chdir(repo_directory)
click.echo("Check for updates...")
local = subprocess.check_output('git rev-parse master'.split()).strip()
remote = subprocess.check_output(
'git ls-remote https://github.com/tldr-pages/tldr/ HEAD'.split()
).split... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def init():
"""Init config file.""" |
default_config_path = path.join(
(os.environ.get('TLDR_CONFIG_DIR') or path.expanduser('~')),
'.tldrrc')
if path.exists(default_config_path):
click.echo("There is already a config file exists, "
"skip initializing it.")
else:
repo_path = click.prompt("Inpu... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def locate(command, on):
"""Locate the command's man page.""" |
location = find_page_location(command, on)
click.echo(location) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def map_to(self, attrname, tablename=None, selectable=None, schema=None, base=None, mapper_args=util.immutabledict()):
"""Configure a mapping to the given attrna... |
if attrname in self._cache:
raise SQLSoupError(
"Attribute '%s' is already mapped to '%s'" % (
attrname,
class_mapper(self._cache[attrname]).mapped_table
))
if tablename is not None:
if not isinstance(tablename, basest... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def map(self, selectable, base=None, **mapper_args):
"""Map a selectable directly. The class and its mapping are not cached and will be discarded once dereferenc... |
return _class_for_table(
self.session,
self.engine,
selectable,
base or self.base,
mapper_args
) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def with_labels(self, selectable, base=None, **mapper_args):
"""Map a selectable directly, wrapping the selectable in a subquery with labels. The class and its m... |
# TODO give meaningful aliases
return self.map(
expression._clause_element_as_expr(selectable).
select(use_labels=True).
alias('foo'), base=base, **mapper_args) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def left(self, f, n=1):
"""return the nearest n features strictly to the left of a Feature f. Overlapping features are not considered as to the left. f: a Featur... |
intervals = self.intervals[f.chrom]
if intervals == []: return []
iright = binsearch_left_start(intervals, f.start, 0 , len(intervals)) + 1
ileft = binsearch_left_start(intervals, f.start - self.max_len[f.chrom] - 1, 0, 0)
results = sorted((distance(other, f), other) for othe... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def right(self, f, n=1):
"""return the nearest n features strictly to the right of a Feature f. Overlapping features are not considered as to the right. f: a Fea... |
intervals = self.intervals[f.chrom]
ilen = len(intervals)
iright = binsearch_right_end(intervals, f.end, 0, ilen)
results = []
while iright < ilen:
i = len(results)
if i > n:
if distance(f, results[i - 1]) != distance(f, results[i - 2]):
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def upstream(self, f, n=1):
"""find n upstream features where upstream is determined by the strand of the query Feature f Overlapping features are not considered... |
if f.strand == -1:
return self.right(f, n)
return self.left(f, n) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def downstream(self, f, n=1):
"""find n downstream features where downstream is determined by the strand of the query Feature f Overlapping features are not cons... |
if f.strand == -1:
return self.left(f, n)
return self.right(f, n) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def sequence(db, chrom, start, end):
""" return the sequence for a region using the UCSC DAS server. note the start is 1-based each feature will have it's own .s... |
url = "http://genome.ucsc.edu/cgi-bin/das/%s" % db
url += "/dna?segment=%s:%i,%i"
xml = U.urlopen(url % (chrom, start, end)).read()
return _seq_from_xml(xml) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def set_table(genome, table, table_name, connection_string, metadata):
""" alter the table to work between different dialects """ |
table = Table(table_name, genome._metadata, autoload=True,
autoload_with=genome.bind, extend_existing=True)
#print "\t".join([c.name for c in table.columns])
# need to prefix the indexes with the table name to avoid collisions
for i, idx in enumerate(table.indexes):
idx.nam... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def mirror(self, tables, dest_url):
""" miror a set of `tables` from `dest_url` Returns a new Genome object Parameters tables : list an iterable of tables dest_u... |
from mirror import mirror
return mirror(self, tables, dest_url) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def dataframe(self, table):
""" create a pandas dataframe from a table or query Parameters table : table a table in this database or a query limit: integer an in... |
from pandas import DataFrame
if isinstance(table, six.string_types):
table = getattr(self, table)
try:
rec = table.first()
except AttributeError:
rec = table[0]
if hasattr(table, "all"):
records = table.all()
else:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def david_go(refseq_list, annot=('SP_PIR_KEYWORDS', 'GOTERM_BP_FAT', 'GOTERM_CC_FAT', 'GOTERM_MF_FAT')):
""" open a web-browser to the DAVID online enrichment to... |
URL = "http://david.abcc.ncifcrf.gov/api.jsp?type=REFSEQ_MRNA&ids=%s&tool=term2term&annot="
import webbrowser
webbrowser.open(URL % ",".join(set(refseq_list)) + ",".join(annot)) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def bin_query(self, table, chrom, start, end):
""" perform an efficient spatial query using the bin column if available. The possible bins are calculated from th... |
if isinstance(table, six.string_types):
table = getattr(self, table)
try:
tbl = table._table
except AttributeError:
tbl = table.column_descriptions[0]['type']._table
q = table.filter(tbl.c.chrom == chrom)
if hasattr(tbl.c, "bin"):
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def upstream(self, table, chrom_or_feat, start=None, end=None, k=1):
""" Return k-nearest upstream features Parameters table : str or table table against which t... |
res = self.knearest(table, chrom_or_feat, start, end, k, "up")
end = getattr(chrom_or_feat, "end", end)
start = getattr(chrom_or_feat, "start", start)
rev = getattr(chrom_or_feat, "strand", "+") == "-"
if rev:
return [x for x in res if x.end > start]
else:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def knearest(self, table, chrom_or_feat, start=None, end=None, k=1, _direction=None):
""" Return k-nearest features Parameters table : str or table table against... |
assert _direction in (None, "up", "down")
# they sent in a feature
if start is None:
assert end is None
chrom, start, end = chrom_or_feat.chrom, chrom_or_feat.start, chrom_or_feat.end
# if the query is directional and the feature as a strand,
# ... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def annotate(self, fname, tables, feature_strand=False, in_memory=False, header=None, out=sys.stdout, parallel=False):
""" annotate a file with a number of table... |
from .annotate import annotate
return annotate(self, fname, tables, feature_strand, in_memory, header=header,
out=out, parallel=parallel) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def bins(start, end):
""" Get all the bin numbers for a particular interval defined by (start, end] """ |
if end - start < 536870912:
offsets = [585, 73, 9, 1]
else:
raise BigException
offsets = [4681, 585, 73, 9, 1]
binFirstShift = 17
binNextShift = 3
start = start >> binFirstShift
end = (end - 1) >> binFirstShift
bins = [1]
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def _find_filepath_in_roots(filename):
"""Look for filename in all MEDIA_ROOTS, and return the first one found.""" |
for root in settings.DJANGO_STATIC_MEDIA_ROOTS:
filepath = _filename2filepath(filename, root)
if os.path.isfile(filepath):
return filepath, root
# havent found it in DJANGO_STATIC_MEDIA_ROOTS look for apps' files if we're
# in DEBUG mode
if settings.DEBUG:
try:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def default_combine_filenames_generator(filenames, max_length=40):
"""Return a new filename to use as the combined file name for a bunch of files. A precondition... |
path = None
names = []
extension = None
timestamps = []
for filename in filenames:
name = os.path.basename(filename)
if not extension:
extension = os.path.splitext(name)[1]
elif os.path.splitext(name)[1] != extension:
raise ValueError("Can't combine m... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def overlaps(self, other):
""" check for overlap with the other interval """ |
if self.chrom != other.chrom: return False
if self.start >= other.end: return False
if other.start >= self.end: return False
return True |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def is_upstream_of(self, other):
""" check if this is upstream of the `other` interval taking the strand of the other interval into account """ |
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "+":
return self.end <= other.start
# other feature is on - strand, so this must have higher start
return self.start >= other.end |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def gene_features(self):
""" return a list of features for the gene features of this object. This would include exons, introns, utrs, etc. """ |
nm, strand = self.gene_name, self.strand
feats = [(self.chrom, self.start, self.end, nm, strand, 'gene')]
for feat in ('introns', 'exons', 'utr5', 'utr3', 'cdss'):
fname = feat[:-1] if feat[-1] == 's' else feat
res = getattr(self, feat)
if res is None or all(... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def tss(self, up=0, down=0):
""" Return a start, end tuple of positions around the transcription-start site Parameters up : int if greature than 0, the strand is... |
if not self.is_gene_pred: return None
tss = self.txEnd if self.strand == '-' else self.txStart
start, end = tss, tss
if self.strand == '+':
start -= up
end += down
else:
start += up
end -= down
start, end = end, start
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def promoter(self, up=2000, down=0):
""" Return a start, end tuple of positions for the promoter region of this gene Parameters up : int this distance upstream t... |
if not self.is_gene_pred: return None
return self.tss(up=up, down=down) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def cds(self):
"""just the parts of the exons that are translated""" |
ces = self.coding_exons
if len(ces) < 1: return ces
ces[0] = (self.cdsStart, ces[0][1])
ces[-1] = (ces[-1][0], self.cdsEnd)
assert all((s < e for s, e in ces))
return ces |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def is_downstream_of(self, other):
""" return a boolean indicating whether this feature is downstream of `other` taking the strand of other into account """ |
if self.chrom != other.chrom: return None
if getattr(other, "strand", None) == "-":
# other feature is on - strand, so this must have higher start
return self.end <= other.start
return self.start >= other.end |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def utr5(self):
""" return the 5' UTR if appropriate """ |
if not self.is_coding or len(self.exons) < 2: return (None, None)
if self.strand == "+":
s, e = (self.txStart, self.cdsStart)
else:
s, e = (self.cdsEnd, self.txEnd)
if s == e: return (None, None)
return s, e |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def sequence(self, per_exon=False):
""" Return the sequence for this feature. if per-exon is True, return an array of exon sequences This sequence is never rever... |
db = self.db
if not per_exon:
start = self.txStart + 1
return _sequence(db, self.chrom, start, self.txEnd)
else:
# TODO: use same strategy as cds_sequence to reduce # of requests.
seqs = []
for start, end in self.exons:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def ncbi_blast(self, db="nr", megablast=True, sequence=None):
""" perform an NCBI blast against the sequence of this feature """ |
import requests
requests.defaults.max_retries = 4
assert sequence in (None, "cds", "mrna")
seq = self.sequence() if sequence is None else ("".join(self.cds_sequence if sequence == "cds" else self.mrna_sequence))
r = requests.post('http://blast.ncbi.nlm.nih.gov/Blast.cgi',
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def blat(self, db=None, sequence=None, seq_type="DNA"):
""" make a request to the genome-browsers BLAT interface sequence is one of None, "mrna", "cds" returns a... |
from . blat_blast import blat, blat_all
assert sequence in (None, "cds", "mrna")
seq = self.sequence() if sequence is None else ("".join(self.cds_sequence if sequence == "cds" else self.mrna_sequence))
if isinstance(db, (tuple, list)):
return blat_all(seq, self.gene_name, db... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def bed(self, *attrs, **kwargs):
""" return a bed formatted string of this feature """ |
exclude = ("chrom", "start", "end", "txStart", "txEnd", "chromStart",
"chromEnd")
if self.is_gene_pred:
return self.bed12(**kwargs)
return "\t".join(map(str, (
[self.chrom, self.start, self.end] +
[getattr(self, attr) for attr in att... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def dereference_url(url):
""" Makes a HEAD request to find the final destination of a URL after following any redirects """ |
res = open_url(url, method='HEAD')
res.close()
return res.url |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def read(url, **kwargs):
""" Read the contents of a URL into memory, return """ |
response = open_url(url, **kwargs)
try:
return response.read()
finally:
response.close() |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def check_extracted_paths(namelist, subdir=None):
""" Check whether zip file paths are all relative, and optionally in a specified subdirectory, raises an except... |
def relpath(p):
# relpath strips a trailing sep
# Windows paths may also use unix sep
q = os.path.relpath(p)
if p.endswith(os.path.sep) or p.endswith('/'):
q += os.path.sep
return q
parent = os.path.abspath('.')
if subdir:
if os.path.isabs(subdir... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_as_local_path(path, overwrite, progress=0, httpuser=None, httppassword=None):
""" Automatically handle local and remote URLs, files and directories path:... |
m = re.match('([A-Za-z]+)://', path)
if m:
# url_open handles multiple protocols so don't bother validating
log.debug('Detected URL protocol: %s', m.group(1))
# URL should use / as the pathsep
localpath = path.split('/')[-1]
if not localpath:
raise FileExcep... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def create(fs, channels, application):
"""Allocates and initializes an encoder state.""" |
result_code = ctypes.c_int()
result = _create(fs, channels, application, ctypes.byref(result_code))
if result_code.value is not constants.OK:
raise OpusError(result_code.value)
return result |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def encode(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame Returns string output payload """ |
pcm = ctypes.cast(pcm, c_int16_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise OpusError(result)
return array.array('c', data[:result]).tostring() |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def encode_float(encoder, pcm, frame_size, max_data_bytes):
"""Encodes an Opus frame from floating point input""" |
pcm = ctypes.cast(pcm, c_float_pointer)
data = (ctypes.c_char * max_data_bytes)()
result = _encode_float(encoder, pcm, frame_size, data, max_data_bytes)
if result < 0:
raise OpusError(result)
return array.array('c', data[:result]).tostring() |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
| def __parse_tostr(self, text, **kwargs):
'''Builds and returns the MeCab function for parsing Unicode text.
Args:
fn_name: MeCab function name that determines the function
behavior, either 'mecab_sparse_tostr' or
'mecab_nbest_sparse_tostr'.
Returns:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
| def parse(self, text, **kwargs):
'''Parse the given text and return result from MeCab.
:param text: the text to parse.
:type text: str
:param as_nodes: return generator of MeCabNodes if True;
or string if False.
:type as_nodes: bool, defaults to False
:param ... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def generate(tagGroups, terms):
""" create Tag Groups and Child Tags using data from terms dict """ |
rv = []
for pid in tagGroups:
# In testing we may not have complete set
if pid not in terms.keys():
continue
groupData = terms[pid]
groupName = "[%s] %s" % (pid, groupData['name'])
groupDesc = groupData['desc']
children = []
group = dict(nam... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def _handle_args(self, cmd, args):
""" We need to support deprecated behaviour for now which makes this quite complicated Current behaviour: - install: Installs ... |
if cmd == 'install':
if args.upgrade:
# Current behaviour: install or upgrade
if args.initdb or args.upgradedb:
raise Stop(10, (
'Deprecated --initdb --upgradedb flags '
'are incompatible with --upgr... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def handle_database(self):
""" Handle database initialisation and upgrade, taking into account command line arguments """ |
# TODO: When initdb and upgradedb are dropped we can just test
# managedb, but for backwards compatibility we need to support
# initdb without upgradedb and vice-versa
if self.args.initdb or self.args.upgradedb:
db = DbAdmin(self.dir, None, self.args, self.external)
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def run(self, command):
""" Runs a command as if from the command-line without the need for using popen or subprocess """ |
if isinstance(command, basestring):
command = command.split()
else:
command = list(command)
self.external.omero_cli(command) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def sort_schemas(schemas):
"""Sort a list of SQL schemas in order""" |
def keyfun(v):
x = SQL_SCHEMA_REGEXP.match(v).groups()
# x3: 'DEV' should come before ''
return (int(x[0]), x[1], int(x[2]) if x[2] else None,
x[3] if x[3] else 'zzz', int(x[4]))
return sorted(schemas, key=keyfun) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_schema_files(files):
""" Parse a list of SQL files and return a dictionary of valid schema files where each key is a valid schema file and the correspo... |
f_dict = {}
for f in files:
root, ext = os.path.splitext(f)
if ext != ".sql":
continue
vto, vfrom = os.path.split(root)
vto = os.path.split(vto)[1]
if is_schema(vto) and is_schema(vfrom):
f_dict[f] = (vfrom, vto)
return f_dict |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def dump(self):
""" Dump the database using the postgres custom format """ |
dumpfile = self.args.dumpfile
if not dumpfile:
db, env = self.get_db_args_env()
dumpfile = fileutils.timestamp_filename(
'omero-database-%s' % db['name'], 'pgdump')
log.info('Dumping database to %s', dumpfile)
if not self.args.dry_run:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_db_args_env(self):
""" Get a dictionary of database connection parameters, and create an environment for running postgres commands. Falls back to omego d... |
db = {
'name': self.args.dbname,
'host': self.args.dbhost,
'user': self.args.dbuser,
'pass': self.args.dbpass
}
if not self.args.no_db_config:
try:
c = self.external.get_config(force=True)
except Except... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def psql(self, *psqlargs):
""" Run a psql command """ |
db, env = self.get_db_args_env()
args = [
'-v', 'ON_ERROR_STOP=on',
'-d', db['name'],
'-h', db['host'],
'-U', db['user'],
'-w', '-A', '-t'
] + list(psqlargs)
stdout, stderr = External.run('psql', args, capturestd=True, env... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def pgdump(self, *pgdumpargs):
""" Run a pg_dump command """ |
db, env = self.get_db_args_env()
args = ['-d', db['name'], '-h', db['host'], '-U', db['user'], '-w'
] + list(pgdumpargs)
stdout, stderr = External.run(
'pg_dump', args, capturestd=True, env=env)
if stderr:
log.warn('stderr: %s', stderr)
l... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def set_server_dir(self, dir):
""" Set the directory of the server to be controlled """ |
self.dir = os.path.abspath(dir)
config = os.path.join(self.dir, 'etc', 'grid', 'config.xml')
self.configured = os.path.exists(config) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_config(self, force=False):
""" Returns a dictionary of all config.xml properties If `force = True` then ignore any cached state and read config.xml if po... |
if not force and not self.has_config():
raise Exception('No config file')
configxml = os.path.join(self.dir, 'etc', 'grid', 'config.xml')
if not os.path.exists(configxml):
raise Exception('No config file')
try:
# Attempt to open config.xml read-only... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def setup_omero_cli(self):
""" Imports the omero CLI module so that commands can be run directly. Note Python does not allow a module to be imported multiple tim... |
if not self.dir:
raise Exception('No server directory set')
if 'omero.cli' in sys.modules:
raise Exception('omero.cli can only be imported once')
log.debug("Setting up omero CLI")
lib = os.path.join(self.dir, "lib", "python")
if not os.path.exists(lib):... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def setup_previous_omero_env(self, olddir, savevarsfile):
""" Create a copy of the current environment for interacting with the current OMERO server installation... |
env = self.get_environment(savevarsfile)
def addpath(varname, p):
if not os.path.exists(p):
raise Exception("%s does not exist!" % p)
current = env.get(varname)
if current:
env[varname] = p + os.pathsep + current
else:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def omero_cli(self, command):
""" Runs a command as if from the OMERO command-line without the need for using popen or subprocess. """ |
assert isinstance(command, list)
if not self.cli:
raise Exception('omero.cli not initialised')
log.info("Invoking CLI [current environment]: %s", " ".join(command))
self.cli.invoke(command, strict=True) |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def run(exe, args, capturestd=False, env=None):
""" Runs an executable with an array of arguments, optionally in the specified environment. Returns stdout and st... |
command = [exe] + args
if env:
log.info("Executing [custom environment]: %s", " ".join(command))
else:
log.info("Executing : %s", " ".join(command))
start = time.time()
# Temp files will be automatically deleted on close()
# If run() throws the g... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
| def string_support(py3enc):
'''Create byte-to-string and string-to-byte conversion functions for
internal use.
:param py3enc: Encoding used by Python 3 environment.
:type py3enc: str
'''
if sys.version < '3':
def bytes2str(b):
'''Identity, returns the argument string (bytes)... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
| def splitter_support(py2enc):
'''Create tokenizer for use in boundary constraint parsing.
:param py2enc: Encoding used by Python 2 environment.
:type py2enc: str
'''
if sys.version < '3':
def _fn_sentence(pattern, sentence):
if REGEXTYPE == type(pattern):
if patt... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def upsert(self, doc, namespace, timestamp, update_spec=None):
"""Insert a document into Elasticsearch.""" |
index, doc_type = self._index_and_mapping(namespace)
# No need to duplicate '_id' in source document
doc_id = u(doc.pop("_id"))
metadata = {
'ns': namespace,
'_ts': timestamp
}
# Index the source document, using lowercase namespace as index name.... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def bulk_upsert(self, docs, namespace, timestamp):
"""Insert multiple documents into Elasticsearch.""" |
def docs_to_upsert():
doc = None
for doc in docs:
# Remove metadata and redundant _id
index, doc_type = self._index_and_mapping(namespace)
doc_id = u(doc.pop("_id"))
document_action = {
'_index': index,
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def remove(self, document_id, namespace, timestamp):
"""Remove a document from Elasticsearch.""" |
index, doc_type = self._index_and_mapping(namespace)
action = {
'_op_type': 'delete',
'_index': index,
'_type': doc_type,
'_id': u(document_id)
}
meta_action = {
'_op_type': 'delete',
'_index': self.meta_index_nam... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def send_buffered_operations(self):
"""Send buffered operations to Elasticsearch. This method is periodically called by the AutoCommitThread. """ |
with self.lock:
try:
action_buffer = self.BulkBuffer.get_buffer()
if action_buffer:
successes, errors = bulk(self.elastic, action_buffer)
LOG.debug("Bulk request finished, successfully sent %d "
"o... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_last_doc(self):
"""Get the most recently modified document from Elasticsearch. This method is used to help define a time window within which documents ma... |
try:
result = self.elastic.search(
index=self.meta_index_name,
body={
"query": {"match_all": {}},
"sort": [{"_ts": "desc"}],
},
size=1
)["hits"]["hits"]
for r in result:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_type_signature(sig):
""" Parse a type signature """ |
match = TYPE_SIG_RE.match(sig.strip())
if not match:
raise RuntimeError('Type signature invalid, got ' + sig)
groups = match.groups()
typ = groups[0]
generic_types = groups[1]
if not generic_types:
generic_types = []
else:
generic_types = split_sig(generic_types[1:-1... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def parse_attr_signature(sig):
""" Parse an attribute signature """ |
match = ATTR_SIG_RE.match(sig.strip())
if not match:
raise RuntimeError('Attribute signature invalid, got ' + sig)
name, _, params = match.groups()
if params is not None and params.strip() != '':
params = split_sig(params)
params = [parse_param_signature(x) for x in params]
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def get_msdn_ref(name):
""" Try and create a reference to a type on MSDN """ |
in_msdn = False
if name in MSDN_VALUE_TYPES:
name = MSDN_VALUE_TYPES[name]
in_msdn = True
if name.startswith('System.'):
in_msdn = True
if in_msdn:
link = name.split('<')[0]
if link in MSDN_LINK_MAP:
link = MSDN_LINK_MAP[link]
else:
... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def shorten_type(typ):
""" Shorten a type. E.g. drops 'System.' """ |
offset = 0
for prefix in SHORTEN_TYPE_PREFIXES:
if typ.startswith(prefix):
if len(prefix) > offset:
offset = len(prefix)
return typ[offset:] |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.