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brentp/cruzdb | cruzdb/models.py | Interval.overlaps | 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 | python | 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 | [
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brentp/cruzdb | cruzdb/models.py | Interval.is_upstream_of | 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
... | python | def is_upstream_of(self, other):
"""
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"""
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if getattr(other, "strand", None) == "+":
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brentp/cruzdb | cruzdb/models.py | Interval.distance | def distance(self, other_or_start=None, end=None, features=False):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
the start ... | python | def distance(self, other_or_start=None, end=None, features=False):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute indicating
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brentp/cruzdb | cruzdb/models.py | ABase.exons | def exons(self):
"""
return a list of exons [(start, stop)] for this object if appropriate
"""
# drop the trailing comma
if not self.is_gene_pred: return []
if hasattr(self, "exonStarts"):
try:
starts = (long(s) for s in self.exonStarts[:-1].sp... | python | def exons(self):
"""
return a list of exons [(start, stop)] for this object if appropriate
"""
# drop the trailing comma
if not self.is_gene_pred: return []
if hasattr(self, "exonStarts"):
try:
starts = (long(s) for s in self.exonStarts[:-1].sp... | [
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brentp/cruzdb | cruzdb/models.py | ABase.gene_features | 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 ('i... | python | 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 ('i... | [
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brentp/cruzdb | cruzdb/models.py | ABase.tss | 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 used to add this many upstream
bases in the appropriate direction
... | python | 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 used to add this many upstream
bases in the appropriate direction
... | [
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brentp/cruzdb | cruzdb/models.py | ABase.promoter | 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 that is considered the promoter
down : int
the strand is used to add... | python | 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 that is considered the promoter
down : int
the strand is used to add... | [
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the strand is used to add this many downstream bases into the gene. | [
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brentp/cruzdb | cruzdb/models.py | ABase.coding_exons | def coding_exons(self):
"""
includes the entire exon as long as any of it is > cdsStart and <
cdsEnd
"""
# drop the trailing comma
starts = (long(s) for s in self.exonStarts[:-1].split(","))
ends = (long(s) for s in self.exonEnds[:-1].split(","))
return [(... | python | def coding_exons(self):
"""
includes the entire exon as long as any of it is > cdsStart and <
cdsEnd
"""
# drop the trailing comma
starts = (long(s) for s in self.exonStarts[:-1].split(","))
ends = (long(s) for s in self.exonEnds[:-1].split(","))
return [(... | [
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brentp/cruzdb | cruzdb/models.py | ABase.cds | 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 | python | 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 | [
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brentp/cruzdb | cruzdb/models.py | ABase.is_downstream_of | 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 ... | python | 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 ... | [
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brentp/cruzdb | cruzdb/models.py | ABase.features | def features(self, other_start, other_end):
"""
return e.g. "intron;exon" if the other_start, end overlap introns and
exons
"""
# completely encases gene.
if other_start <= self.start and other_end >= self.end:
return ['gene' if self.cdsStart != self.cdsEnd el... | python | def features(self, other_start, other_end):
"""
return e.g. "intron;exon" if the other_start, end overlap introns and
exons
"""
# completely encases gene.
if other_start <= self.start and other_end >= self.end:
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brentp/cruzdb | cruzdb/models.py | ABase.upstream | def upstream(self, distance):
"""
return the (start, end) of the region before the geneStart
"""
if getattr(self, "strand", None) == "+":
e = self.start
s = e - distance
else:
s = self.end
e = s + distance
return self._xstre... | python | def upstream(self, distance):
"""
return the (start, end) of the region before the geneStart
"""
if getattr(self, "strand", None) == "+":
e = self.start
s = e - distance
else:
s = self.end
e = s + distance
return self._xstre... | [
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brentp/cruzdb | cruzdb/models.py | ABase.utr5 | 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 ... | python | 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)
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s, e = (self.cdsEnd, self.txEnd)
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brentp/cruzdb | cruzdb/models.py | ABase.sequence | 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 reverse complemented
"""
db = self.db
if not per_exon:
start = self.txStart + 1
retu... | python | 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 reverse complemented
"""
db = self.db
if not per_exon:
start = self.txStart + 1
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brentp/cruzdb | cruzdb/models.py | ABase.ncbi_blast | 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 el... | python | 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")
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brentp/cruzdb | cruzdb/models.py | ABase.blat | 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 list of features that are hits to this sequence.
"""
from . blat_blast import blat, blat_all
assert se... | python | 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 list of features that are hits to this sequence.
"""
from . blat_blast import blat, blat_all
assert se... | [
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brentp/cruzdb | cruzdb/models.py | ABase.bed | def bed(self, *attrs, **kwargs):
"""
return a bed formatted string of this feature
"""
exclude = ("chrom", "start", "end", "txStart", "txEnd", "chromStart",
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if self.is_gene_pred:
return self.bed12(**kwargs)
return "\t".join(map(str,... | python | 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:
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brentp/cruzdb | cruzdb/models.py | ABase.bed12 | def bed12(self, score="0", rgb="."):
"""
return a bed12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
representation of this interval
"""
if not self.is_gene_pred:
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"""
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brentp/cruzdb | cruzdb/models.py | ABase.localize | def localize(self, *positions, **kwargs):
"""
convert global coordinate(s) to local taking
introns into account and cds/tx-Start depending on cdna=True kwarg
"""
cdna = kwargs.get('cdna', False)
# TODO: account for strand ?? add kwarg ??
# if it's to the CDNA, the... | python | def localize(self, *positions, **kwargs):
"""
convert global coordinate(s) to local taking
introns into account and cds/tx-Start depending on cdna=True kwarg
"""
cdna = kwargs.get('cdna', False)
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brentp/cruzdb | cruzdb/models.py | cpgIslandExt.distance | def distance(self, other_or_start=None, end=None, features="unused",
shore_dist=3000):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute i... | python | def distance(self, other_or_start=None, end=None, features="unused",
shore_dist=3000):
"""
check the distance between this an another interval
Parameters
----------
other_or_start : Interval or int
either an integer or an Interval with a start attribute i... | [
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brentp/cruzdb | cruzdb/annotate.py | annotate | def annotate(g, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, _chrom=None, parallel=False):
"""
annotate bed file in fname with tables.
distances are integers for distance. and intron/exon/utr5 etc for gene-pred
tables. if the annotation features have a stran... | python | def annotate(g, fname, tables, feature_strand=False, in_memory=False,
header=None, out=sys.stdout, _chrom=None, parallel=False):
"""
annotate bed file in fname with tables.
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ome/omego | omego/main.py | entry_point | def entry_point():
"""
External entry point which calls main() and
if Stop is raised, calls sys.exit()
"""
try:
main("omego", items=[
(InstallCommand.NAME, InstallCommand),
(UpgradeCommand.NAME, UpgradeCommand),
(ConvertCommand.NAME, ConvertCommand),
... | python | def entry_point():
"""
External entry point which calls main() and
if Stop is raised, calls sys.exit()
"""
try:
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... | [
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ome/omego | omego/fileutils.py | open_url | def open_url(url, httpuser=None, httppassword=None, method=None):
"""
Open a URL using an opener that will simulate a browser user-agent
url: The URL
httpuser, httppassword: HTTP authentication credentials (either both or
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method: The HTTP method
Caller is reponsi... | python | def open_url(url, httpuser=None, httppassword=None, method=None):
"""
Open a URL using an opener that will simulate a browser user-agent
url: The URL
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ome/omego | omego/fileutils.py | dereference_url | def dereference_url(url):
"""
Makes a HEAD request to find the final destination of a URL after
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"""
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res.close()
return res.url | python | def dereference_url(url):
"""
Makes a HEAD request to find the final destination of a URL after
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ome/omego | omego/fileutils.py | read | def read(url, **kwargs):
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response = open_url(url, **kwargs)
try:
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finally:
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"""
Read the contents of a URL into memory, return
"""
response = open_url(url, **kwargs)
try:
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ome/omego | omego/fileutils.py | download | def download(url, filename=None, print_progress=0, delete_fail=True,
**kwargs):
"""
Download a file, optionally printing a simple progress bar
url: The URL to download
filename: The filename to save to, default is to use the URL basename
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"""
Download a file, optionally printing a simple progress bar
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filename: The filename to save to, default is to use the URL basename
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ome/omego | omego/fileutils.py | rename_backup | def rename_backup(name, suffix='.bak'):
"""
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"""
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ome/omego | omego/fileutils.py | timestamp_filename | def timestamp_filename(basename, ext=None):
"""
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"""
Return a string of the form [basename-TIMESTAMP.ext]
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dt = datetime.now().strftime('%Y%m%d-%H%M%S-%f')
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ome/omego | omego/fileutils.py | check_extracted_paths | def check_extracted_paths(namelist, subdir=None):
"""
Check whether zip file paths are all relative, and optionally in a
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namelist: A list of paths from the zip file
subdir: If specified then check whether all paths in the zip file are
under t... | python | def check_extracted_paths(namelist, subdir=None):
"""
Check whether zip file paths are all relative, and optionally in a
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ome/omego | omego/fileutils.py | unzip | def unzip(filename, match_dir=False, destdir=None):
"""
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ome/omego | omego/fileutils.py | zip | def zip(filename, paths, strip_prefix=''):
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ome/omego | omego/fileutils.py | get_as_local_path | def get_as_local_path(path, overwrite, progress=0,
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svartalf/python-opus | opus/api/encoder.py | create | 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 | python | 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 | [
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svartalf/python-opus | opus/api/encoder.py | encode_float | def encode_float(encoder, pcm, frame_size, max_data_bytes):
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buruzaemon/natto-py | natto/mecab.py | MeCab.__parse_tostr | def __parse_tostr(self, text, **kwargs):
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Args:
fn_name: MeCab function name that determines the function
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Returns:
... | python | def __parse_tostr(self, text, **kwargs):
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buruzaemon/natto-py | natto/mecab.py | MeCab.parse | def parse(self, text, **kwargs):
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:param text: the text to parse.
:type text: str
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:param ... | python | def parse(self, text, **kwargs):
'''Parse the given text and return result from MeCab.
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ome/omego | omego/convert.py | parse | def parse(filename, MAX_TERM_COUNT=1000):
"""
MAX_TERM_COUNT = 10000 # There are 39,000 terms in the GO!
"""
with open(filename, "r") as f:
termId = None
name = None
desc = None
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termCount = 0
for l in f.readlines():
if l.st... | python | def parse(filename, MAX_TERM_COUNT=1000):
"""
MAX_TERM_COUNT = 10000 # There are 39,000 terms in the GO!
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ome/omego | omego/convert.py | generate | 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" ... | python | def generate(tagGroups, terms):
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ome/omego | omego/upgrade.py | Install._handle_args | def _handle_args(self, cmd, args):
"""
We need to support deprecated behaviour for now which makes this
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Current behaviour:
- install: Installs a new server, existing server causes an error
- install --upgrade: Installs or upgrades a server
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ome/omego | omego/upgrade.py | Install.get_server_dir | def get_server_dir(self):
"""
Either downloads and/or unzips the server if necessary
return: the directory of the unzipped server
"""
if not self.args.server:
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raise Stop(0, 'Unzip disabled, exiting')
log.info('Downl... | python | def get_server_dir(self):
"""
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ome/omego | omego/upgrade.py | Install.handle_database | def handle_database(self):
"""
Handle database initialisation and upgrade, taking into account
command line arguments
"""
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# initdb without... | python | def handle_database(self):
"""
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ome/omego | omego/upgrade.py | Install.run | 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(co... | python | def run(self, command):
"""
Runs a command as if from the command-line
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ome/omego | omego/upgrade.py | Install.bin | def bin(self, command):
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ome/omego | omego/upgrade.py | Install.symlink_check_and_set | def symlink_check_and_set(self):
"""
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If `--sym` was not specified and OMERO-CURRENT exists in the current
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"""
if self.args.sym == '':
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"""
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def inner(func, obj):
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raise OpusError(result_code)
return result_code
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"""Query encoder/decoder with a request value"""
def inner(func, obj):
result_code = func(obj, request)
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ome/omego | omego/db.py | sort_schemas | 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,
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return sorted(schem... | python | 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,
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ome/omego | omego/db.py | parse_schema_files | 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 corresponding value is
a tuple containing the source and the target schema.
"""
f_dict = {}
for f in files:
root, ext = os.path.spl... | python | def parse_schema_files(files):
"""
Parse a list of SQL files and return a dictionary of valid schema
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"""
f_dict = {}
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ome/omego | omego/db.py | DbAdmin.dump | 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(
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... | python | 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(
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"""
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"""
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ome/omego | omego/db.py | DbAdmin.psql | def psql(self, *psqlargs):
"""
Run a psql command
"""
db, env = self.get_db_args_env()
args = [
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"""
Run a psql command
"""
db, env = self.get_db_args_env()
args = [
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ome/omego | omego/db.py | DbAdmin.pgdump | def pgdump(self, *pgdumpargs):
"""
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args = ['-d', db['name'], '-h', db['host'], '-U', db['user'], '-w'
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stdout, stderr = External.run(
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"""
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db, env = self.get_db_args_env()
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ome/omego | omego/external.py | External.set_server_dir | 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) | python | def set_server_dir(self, dir):
"""
Set the directory of the server to be controlled
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ome/omego | omego/external.py | External.setup_omero_cli | def setup_omero_cli(self):
"""
Imports the omero CLI module so that commands can be run directly.
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"""
Imports the omero CLI module so that commands can be run directly.
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ome/omego | omego/external.py | External.setup_previous_omero_env | 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):
... | python | 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):
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ome/omego | omego/external.py | External.omero_cli | 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... | python | def omero_cli(self, command):
"""
Runs a command as if from the OMERO command-line without the need
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"""
assert isinstance(command, list)
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ome/omego | omego/external.py | External.omero_bin | def omero_bin(self, command):
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Runs the omero command-line client with an array of arguments using the
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"""
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Runs the omero command-line client with an array of arguments using the
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ome/omego | omego/external.py | External.run | def run(exe, args, capturestd=False, env=None):
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Runs an executable with an array of arguments, optionally in the
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Returns stdout and stderr
"""
command = [exe] + args
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buruzaemon/natto-py | natto/support.py | string_support | def string_support(py3enc):
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:param py3enc: Encoding used by Python 3 environment.
:type py3enc: str
'''
if sys.version < '3':
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'''
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.update | def update(self, document_id, update_spec, namespace, timestamp):
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"""
index, doc_type = self._index_and_mapping(namespace)
with self.lock:
# Check if document source is stored in loca... | python | def update(self, document_id, update_spec, namespace, timestamp):
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.upsert | def upsert(self, doc, namespace, timestamp, update_spec=None):
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index, doc_type = self._index_and_mapping(namespace)
# No need to duplicate '_id' in source document
doc_id = u(doc.pop("_id"))
metadata = {
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index, doc_type = self._index_and_mapping(namespace)
# No need to duplicate '_id' in source document
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.bulk_upsert | def bulk_upsert(self, docs, namespace, timestamp):
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.remove | def remove(self, document_id, namespace, timestamp):
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.send_buffered_operations | def send_buffered_operations(self):
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"""
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yougov/elastic-doc-manager | mongo_connector/doc_managers/elastic_doc_manager.py | DocManager.get_last_doc | def get_last_doc(self):
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This method is used to help define a time window within which documents
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"""
try:
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | split_sig | def split_sig(params):
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level = 0
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | parse_method_signature | def parse_method_signature(sig):
""" Parse a method signature of the form: modifier* type name (params) """
match = METH_SIG_RE.match(sig.strip())
if not match:
raise RuntimeError('Method signature invalid: ' + sig)
modifiers, return_type, name, generic_types, params = match.groups()
if para... | python | def parse_method_signature(sig):
""" Parse a method signature of the form: modifier* type name (params) """
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typ, name, _, ... | python | def parse_param_signature(sig):
""" Parse a parameter signature of the form: type name (= default)? """
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | parse_type_signature | 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 = ... | python | 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]
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | parse_attr_signature | def parse_attr_signature(sig):
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""" Parse an attribute signature """
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | get_msdn_ref | def get_msdn_ref(name):
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if name in MSDN_VALUE_TYPES:
name = MSDN_VALUE_TYPES[name]
in_msdn = True
if name.startswith('System.'):
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if in_msdn:
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""" 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
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djungelorm/sphinx-csharp | sphinx_csharp/csharp.py | shorten_type | def shorten_type(typ):
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return typ[offset:] | python | def shorten_type(typ):
""" Shorten a type. E.g. drops 'System.' """
offset = 0
for prefix in SHORTEN_TYPE_PREFIXES:
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buruzaemon/natto-py | natto/option_parse.py | OptionParse.parse_mecab_options | def parse_mecab_options(self, options):
'''Parses the MeCab options, returning them in a dictionary.
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instead.
:options string or dictionary of options to use when instantiating
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'''Parses the MeCab options, returning them in a dictionary.
Lattice-level option has been deprecated; please use marginal or nbest
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buruzaemon/natto-py | natto/option_parse.py | OptionParse.build_options_str | def build_options_str(self, options):
'''Returns a string concatenation of the MeCab options.
Args:
options: dictionary of options to use when instantiating the MeCab
instance.
Returns:
A string concatenation of the options used when instantiatin... | python | def build_options_str(self, options):
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svartalf/python-opus | opus/api/decoder.py | create | def create(fs, channels):
"""Allocates and initializes a decoder state"""
result_code = ctypes.c_int()
result = _create(fs, channels, ctypes.byref(result_code))
if result_code.value is not 0:
raise OpusError(result_code.value)
return result | python | def create(fs, channels):
"""Allocates and initializes a decoder state"""
result_code = ctypes.c_int()
result = _create(fs, channels, ctypes.byref(result_code))
if result_code.value is not 0:
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svartalf/python-opus | opus/api/decoder.py | packet_get_bandwidth | def packet_get_bandwidth(data):
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data_pointer = ctypes.c_char_p(data)
result = _packet_get_bandwidth(data_pointer)
if result < 0:
raise OpusError(result)
return result | python | def packet_get_bandwidth(data):
"""Gets the bandwidth of an Opus packet."""
data_pointer = ctypes.c_char_p(data)
result = _packet_get_bandwidth(data_pointer)
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svartalf/python-opus | opus/api/decoder.py | packet_get_nb_channels | def packet_get_nb_channels(data):
"""Gets the number of channels from an Opus packet"""
data_pointer = ctypes.c_char_p(data)
result = _packet_get_nb_channels(data_pointer)
if result < 0:
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"""Gets the number of channels from an Opus packet"""
data_pointer = ctypes.c_char_p(data)
result = _packet_get_nb_channels(data_pointer)
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svartalf/python-opus | opus/api/decoder.py | packet_get_nb_frames | def packet_get_nb_frames(data, length=None):
"""Gets the number of frames in an Opus packet"""
data_pointer = ctypes.c_char_p(data)
if length is None:
length = len(data)
result = _packet_get_nb_frames(data_pointer, ctypes.c_int(length))
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"""Gets the number of frames in an Opus packet"""
data_pointer = ctypes.c_char_p(data)
if length is None:
length = len(data)
result = _packet_get_nb_frames(data_pointer, ctypes.c_int(length))
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svartalf/python-opus | opus/api/decoder.py | packet_get_samples_per_frame | def packet_get_samples_per_frame(data, fs):
"""Gets the number of samples per frame from an Opus packet"""
data_pointer = ctypes.c_char_p(data)
result = _packet_get_nb_frames(data_pointer, ctypes.c_int(fs))
if result < 0:
raise OpusError(result)
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"""Gets the number of samples per frame from an Opus packet"""
data_pointer = ctypes.c_char_p(data)
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svartalf/python-opus | opus/api/decoder.py | decode | def decode(decoder, data, length, frame_size, decode_fec, channels=2):
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"""
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ome/omego | omego/artifacts.py | JenkinsArtifacts.label_list_parser | def label_list_parser(self, url):
"""
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"""
labels = re.findall('([^/,]+=[^/,]+)', url)
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stevelittlefish/flaskfilemanager | flaskfilemanager/filemanager.py | init | def init(app, register_blueprint=True, url_prefix='/fm', access_control_function=None,
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"""
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stevelittlefish/flaskfilemanager | flaskfilemanager/filemanager.py | get_file | def get_file(path=None, content=None):
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"""
if path is None:
path = request.args.get('path')
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fi... | python | def get_file(path=None, content=None):
"""
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if path is None:
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buruzaemon/natto-py | natto/environment.py | MeCabEnv.__get_charset | def __get_charset(self):
'''Return the character encoding (charset) used internally by MeCab.
Charset is that of the system dictionary used by MeCab. Will defer to
the user-specified MECAB_CHARSET environment variable, if set.
Defaults to shift-jis on Windows.
Defaults t... | python | def __get_charset(self):
'''Return the character encoding (charset) used internally by MeCab.
Charset is that of the system dictionary used by MeCab. Will defer to
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buruzaemon/natto-py | natto/environment.py | MeCabEnv.__get_libpath | def __get_libpath(self):
'''Return the absolute path to the MeCab library.
On Windows, the path to the system dictionary is used to deduce the
path to libmecab.dll.
Otherwise, mecab-config is used find the libmecab shared object or
dynamic library (*NIX or Mac OS, respec... | python | def __get_libpath(self):
'''Return the absolute path to the MeCab library.
On Windows, the path to the system dictionary is used to deduce the
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buruzaemon/natto-py | natto/environment.py | MeCabEnv.__regkey_value | def __regkey_value(self, path, name='', start_key=None):
r'''Return the data of value mecabrc at MeCab HKEY node.
On Windows, the path to the mecabrc as set in the Windows Registry is
used to deduce the path to libmecab.dll.
Returns:
The full path to the mecabrc on W... | python | def __regkey_value(self, path, name='', start_key=None):
r'''Return the data of value mecabrc at MeCab HKEY node.
On Windows, the path to the mecabrc as set in the Windows Registry is
used to deduce the path to libmecab.dll.
Returns:
The full path to the mecabrc on W... | [
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christian-oudard/htmltreediff | htmltreediff/html.py | diff | def diff(old_html, new_html, cutoff=0.0, plaintext=False, pretty=False):
"""Show the differences between the old and new html document, as html.
Return the document html with extra tags added to show changes. Add <ins>
tags around newly added sections, and <del> tags to show sections that have
been del... | python | def diff(old_html, new_html, cutoff=0.0, plaintext=False, pretty=False):
"""Show the differences between the old and new html document, as html.
Return the document html with extra tags added to show changes. Add <ins>
tags around newly added sections, and <del> tags to show sections that have
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | adjusted_ops | def adjusted_ops(opcodes):
"""
Iterate through opcodes, turning them into a series of insert and delete
operations, adjusting indices to account for the size of insertions and
deletions.
>>> def sequence_opcodes(old, new): return difflib.SequenceMatcher(a=old, b=new).get_opcodes()
>>> list(adju... | python | def adjusted_ops(opcodes):
"""
Iterate through opcodes, turning them into a series of insert and delete
operations, adjusting indices to account for the size of insertions and
deletions.
>>> def sequence_opcodes(old, new): return difflib.SequenceMatcher(a=old, b=new).get_opcodes()
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | match_indices | def match_indices(match):
"""Yield index tuples (old_index, new_index) for each place in the match."""
a, b, size = match
for i in range(size):
yield a + i, b + i | python | def match_indices(match):
"""Yield index tuples (old_index, new_index) for each place in the match."""
a, b, size = match
for i in range(size):
yield a + i, b + i | [
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | get_opcodes | def get_opcodes(matching_blocks):
"""Use difflib to get the opcodes for a set of matching blocks."""
sm = difflib.SequenceMatcher(a=[], b=[])
sm.matching_blocks = matching_blocks
return sm.get_opcodes() | python | def get_opcodes(matching_blocks):
"""Use difflib to get the opcodes for a set of matching blocks."""
sm = difflib.SequenceMatcher(a=[], b=[])
sm.matching_blocks = matching_blocks
return sm.get_opcodes() | [
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | match_blocks | def match_blocks(hash_func, old_children, new_children):
"""Use difflib to find matching blocks."""
sm = difflib.SequenceMatcher(
_is_junk,
a=[hash_func(c) for c in old_children],
b=[hash_func(c) for c in new_children],
)
return sm | python | def match_blocks(hash_func, old_children, new_children):
"""Use difflib to find matching blocks."""
sm = difflib.SequenceMatcher(
_is_junk,
a=[hash_func(c) for c in old_children],
b=[hash_func(c) for c in new_children],
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return sm | [
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | get_nonmatching_blocks | def get_nonmatching_blocks(matching_blocks):
"""Given a list of matching blocks, output the gaps between them.
Non-matches have the format (alo, ahi, blo, bhi). This specifies two index
ranges, one in the A sequence, and one in the B sequence.
"""
i = j = 0
for match in matching_blocks:
... | python | def get_nonmatching_blocks(matching_blocks):
"""Given a list of matching blocks, output the gaps between them.
Non-matches have the format (alo, ahi, blo, bhi). This specifies two index
ranges, one in the A sequence, and one in the B sequence.
"""
i = j = 0
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christian-oudard/htmltreediff | htmltreediff/diff_core.py | merge_blocks | def merge_blocks(a_blocks, b_blocks):
"""Given two lists of blocks, combine them, in the proper order.
Ensure that there are no overlaps, and that they are for sequences of the
same length.
"""
# Check sentinels for sequence length.
assert a_blocks[-1][2] == b_blocks[-1][2] == 0 # sentinel size... | python | def merge_blocks(a_blocks, b_blocks):
"""Given two lists of blocks, combine them, in the proper order.
Ensure that there are no overlaps, and that they are for sequences of the
same length.
"""
# Check sentinels for sequence length.
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