partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
train | remove_gaps | skip column if either is a gap | ctbBio/compare_aligned.py | def remove_gaps(A, B):
"""
skip column if either is a gap
"""
a_seq, b_seq = [], []
for a, b in zip(list(A), list(B)):
if a == '-' or a == '.' or b == '-' or b == '.':
continue
a_seq.append(a)
b_seq.append(b)
return ''.join(a_seq), ''.join(b_seq) | def remove_gaps(A, B):
"""
skip column if either is a gap
"""
a_seq, b_seq = [], []
for a, b in zip(list(A), list(B)):
if a == '-' or a == '.' or b == '-' or b == '.':
continue
a_seq.append(a)
b_seq.append(b)
return ''.join(a_seq), ''.join(b_seq) | [
"skip",
"column",
"if",
"either",
"is",
"a",
"gap"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L52-L62 | [
"def",
"remove_gaps",
"(",
"A",
",",
"B",
")",
":",
"a_seq",
",",
"b_seq",
"=",
"[",
"]",
",",
"[",
"]",
"for",
"a",
",",
"b",
"in",
"zip",
"(",
"list",
"(",
"A",
")",
",",
"list",
"(",
"B",
")",
")",
":",
"if",
"a",
"==",
"'-'",
"or",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | compare_seqs | compare pairs of sequences | ctbBio/compare_aligned.py | def compare_seqs(seqs):
"""
compare pairs of sequences
"""
A, B, ignore_gaps = seqs
a, b = A[1], B[1] # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
if ignore_gaps is True:
pident = calc_pident_ignore_gaps(a, b... | def compare_seqs(seqs):
"""
compare pairs of sequences
"""
A, B, ignore_gaps = seqs
a, b = A[1], B[1] # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
if ignore_gaps is True:
pident = calc_pident_ignore_gaps(a, b... | [
"compare",
"pairs",
"of",
"sequences"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L64-L77 | [
"def",
"compare_seqs",
"(",
"seqs",
")",
":",
"A",
",",
"B",
",",
"ignore_gaps",
"=",
"seqs",
"a",
",",
"b",
"=",
"A",
"[",
"1",
"]",
",",
"B",
"[",
"1",
"]",
"# actual sequences",
"if",
"len",
"(",
"a",
")",
"!=",
"len",
"(",
"b",
")",
":",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | compare_seqs_leven | calculate Levenshtein ratio of sequences | ctbBio/compare_aligned.py | def compare_seqs_leven(seqs):
"""
calculate Levenshtein ratio of sequences
"""
A, B, ignore_gaps = seqs
a, b = remove_gaps(A[1], B[1]) # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
pident = lr(a, b) * 100
return A... | def compare_seqs_leven(seqs):
"""
calculate Levenshtein ratio of sequences
"""
A, B, ignore_gaps = seqs
a, b = remove_gaps(A[1], B[1]) # actual sequences
if len(a) != len(b):
print('# reads are not the same length', file=sys.stderr)
exit()
pident = lr(a, b) * 100
return A... | [
"calculate",
"Levenshtein",
"ratio",
"of",
"sequences"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L79-L89 | [
"def",
"compare_seqs_leven",
"(",
"seqs",
")",
":",
"A",
",",
"B",
",",
"ignore_gaps",
"=",
"seqs",
"a",
",",
"b",
"=",
"remove_gaps",
"(",
"A",
"[",
"1",
"]",
",",
"B",
"[",
"1",
"]",
")",
"# actual sequences",
"if",
"len",
"(",
"a",
")",
"!=",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | pairwise_compare | make pairwise sequence comparisons between aligned sequences | ctbBio/compare_aligned.py | def pairwise_compare(afa, leven, threads, print_list, ignore_gaps):
"""
make pairwise sequence comparisons between aligned sequences
"""
# load sequences into dictionary
seqs = {seq[0]: seq for seq in nr_fasta([afa], append_index = True)}
num_seqs = len(seqs)
# define all pairs
pairs = (... | def pairwise_compare(afa, leven, threads, print_list, ignore_gaps):
"""
make pairwise sequence comparisons between aligned sequences
"""
# load sequences into dictionary
seqs = {seq[0]: seq for seq in nr_fasta([afa], append_index = True)}
num_seqs = len(seqs)
# define all pairs
pairs = (... | [
"make",
"pairwise",
"sequence",
"comparisons",
"between",
"aligned",
"sequences"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L91-L110 | [
"def",
"pairwise_compare",
"(",
"afa",
",",
"leven",
",",
"threads",
",",
"print_list",
",",
"ignore_gaps",
")",
":",
"# load sequences into dictionary",
"seqs",
"=",
"{",
"seq",
"[",
"0",
"]",
":",
"seq",
"for",
"seq",
"in",
"nr_fasta",
"(",
"[",
"afa",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | to_dictionary | - convert list of comparisons to dictionary
- print list of pidents (if requested) to stderr | ctbBio/compare_aligned.py | def to_dictionary(pw, print_list):
"""
- convert list of comparisons to dictionary
- print list of pidents (if requested) to stderr
"""
pairs = {}
for p in pw:
a, b, pident = p
if a not in pairs:
pairs[a] = {a: '-'}
if b not in pairs:
pairs[b] = {b... | def to_dictionary(pw, print_list):
"""
- convert list of comparisons to dictionary
- print list of pidents (if requested) to stderr
"""
pairs = {}
for p in pw:
a, b, pident = p
if a not in pairs:
pairs[a] = {a: '-'}
if b not in pairs:
pairs[b] = {b... | [
"-",
"convert",
"list",
"of",
"comparisons",
"to",
"dictionary",
"-",
"print",
"list",
"of",
"pidents",
"(",
"if",
"requested",
")",
"to",
"stderr"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L112-L130 | [
"def",
"to_dictionary",
"(",
"pw",
",",
"print_list",
")",
":",
"pairs",
"=",
"{",
"}",
"for",
"p",
"in",
"pw",
":",
"a",
",",
"b",
",",
"pident",
"=",
"p",
"if",
"a",
"not",
"in",
"pairs",
":",
"pairs",
"[",
"a",
"]",
"=",
"{",
"a",
":",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_pairwise | print matrix of pidents to stdout | ctbBio/compare_aligned.py | def print_pairwise(pw, median = False):
"""
print matrix of pidents to stdout
"""
names = sorted(set([i for i in pw]))
if len(names) != 0:
if '>' in names[0]:
yield ['#'] + [i.split('>')[1] for i in names if '>' in i]
else:
yield ['#'] + names
for a in... | def print_pairwise(pw, median = False):
"""
print matrix of pidents to stdout
"""
names = sorted(set([i for i in pw]))
if len(names) != 0:
if '>' in names[0]:
yield ['#'] + [i.split('>')[1] for i in names if '>' in i]
else:
yield ['#'] + names
for a in... | [
"print",
"matrix",
"of",
"pidents",
"to",
"stdout"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L132-L155 | [
"def",
"print_pairwise",
"(",
"pw",
",",
"median",
"=",
"False",
")",
":",
"names",
"=",
"sorted",
"(",
"set",
"(",
"[",
"i",
"for",
"i",
"in",
"pw",
"]",
")",
")",
"if",
"len",
"(",
"names",
")",
"!=",
"0",
":",
"if",
"'>'",
"in",
"names",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | print_comps | print stats for comparisons | ctbBio/compare_aligned.py | def print_comps(comps):
"""
print stats for comparisons
"""
if comps == []:
print('n/a')
else:
print('# min: %s, max: %s, mean: %s' % \
(min(comps), max(comps), np.mean(comps))) | def print_comps(comps):
"""
print stats for comparisons
"""
if comps == []:
print('n/a')
else:
print('# min: %s, max: %s, mean: %s' % \
(min(comps), max(comps), np.mean(comps))) | [
"print",
"stats",
"for",
"comparisons"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L157-L165 | [
"def",
"print_comps",
"(",
"comps",
")",
":",
"if",
"comps",
"==",
"[",
"]",
":",
"print",
"(",
"'n/a'",
")",
"else",
":",
"print",
"(",
"'# min: %s, max: %s, mean: %s'",
"%",
"(",
"min",
"(",
"comps",
")",
",",
"max",
"(",
"comps",
")",
",",
"np",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | compare_clades | print min. pident within each clade and then matrix of between-clade max. | ctbBio/compare_aligned.py | def compare_clades(pw):
"""
print min. pident within each clade and then matrix of between-clade max.
"""
names = sorted(set([i for i in pw]))
for i in range(0, 4):
wi, bt = {}, {}
for a in names:
for b in pw[a]:
if ';' not in a or ';' not in b:
... | def compare_clades(pw):
"""
print min. pident within each clade and then matrix of between-clade max.
"""
names = sorted(set([i for i in pw]))
for i in range(0, 4):
wi, bt = {}, {}
for a in names:
for b in pw[a]:
if ';' not in a or ';' not in b:
... | [
"print",
"min",
".",
"pident",
"within",
"each",
"clade",
"and",
"then",
"matrix",
"of",
"between",
"-",
"clade",
"max",
"."
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L167-L216 | [
"def",
"compare_clades",
"(",
"pw",
")",
":",
"names",
"=",
"sorted",
"(",
"set",
"(",
"[",
"i",
"for",
"i",
"in",
"pw",
"]",
")",
")",
"for",
"i",
"in",
"range",
"(",
"0",
",",
"4",
")",
":",
"wi",
",",
"bt",
"=",
"{",
"}",
",",
"{",
"}"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | matrix2dictionary | convert matrix to dictionary of comparisons | ctbBio/compare_aligned.py | def matrix2dictionary(matrix):
"""
convert matrix to dictionary of comparisons
"""
pw = {}
for line in matrix:
line = line.strip().split('\t')
if line[0].startswith('#'):
names = line[1:]
continue
a = line[0]
for i, pident in enumerate(line[1:]... | def matrix2dictionary(matrix):
"""
convert matrix to dictionary of comparisons
"""
pw = {}
for line in matrix:
line = line.strip().split('\t')
if line[0].startswith('#'):
names = line[1:]
continue
a = line[0]
for i, pident in enumerate(line[1:]... | [
"convert",
"matrix",
"to",
"dictionary",
"of",
"comparisons"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L218-L239 | [
"def",
"matrix2dictionary",
"(",
"matrix",
")",
":",
"pw",
"=",
"{",
"}",
"for",
"line",
"in",
"matrix",
":",
"line",
"=",
"line",
".",
"strip",
"(",
")",
".",
"split",
"(",
"'\\t'",
")",
"if",
"line",
"[",
"0",
"]",
".",
"startswith",
"(",
"'#'"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | setoption | Set argument parser option. | bootstrap_py/commands.py | def setoption(parser, metadata=None):
"""Set argument parser option."""
parser.add_argument('-v', action='version',
version=__version__)
subparsers = parser.add_subparsers(help='sub commands help')
create_cmd = subparsers.add_parser('create')
create_cmd.add_argument('name',
... | def setoption(parser, metadata=None):
"""Set argument parser option."""
parser.add_argument('-v', action='version',
version=__version__)
subparsers = parser.add_subparsers(help='sub commands help')
create_cmd = subparsers.add_parser('create')
create_cmd.add_argument('name',
... | [
"Set",
"argument",
"parser",
"option",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L12-L51 | [
"def",
"setoption",
"(",
"parser",
",",
"metadata",
"=",
"None",
")",
":",
"parser",
".",
"add_argument",
"(",
"'-v'",
",",
"action",
"=",
"'version'",
",",
"version",
"=",
"__version__",
")",
"subparsers",
"=",
"parser",
".",
"add_subparsers",
"(",
"help"... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | valid_url | Validate url.
:rtype: str
:return: url
:param str url: package homepage url. | bootstrap_py/commands.py | def valid_url(url):
"""Validate url.
:rtype: str
:return: url
:param str url: package homepage url.
"""
regex = re.compile(
r'^(?:http)s?://'
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)+'
r'(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?))'
r'(?:/?|[/?]\S+)$', re.IGNORECA... | def valid_url(url):
"""Validate url.
:rtype: str
:return: url
:param str url: package homepage url.
"""
regex = re.compile(
r'^(?:http)s?://'
r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\.)+'
r'(?:[A-Z]{2,6}\.?|[A-Z0-9-]{2,}\.?))'
r'(?:/?|[/?]\S+)$', re.IGNORECA... | [
"Validate",
"url",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L54-L69 | [
"def",
"valid_url",
"(",
"url",
")",
":",
"regex",
"=",
"re",
".",
"compile",
"(",
"r'^(?:http)s?://'",
"r'(?:(?:[A-Z0-9](?:[A-Z0-9-]{0,61}[A-Z0-9])?\\.)+'",
"r'(?:[A-Z]{2,6}\\.?|[A-Z0-9-]{2,}\\.?))'",
"r'(?:/?|[/?]\\S+)$'",
",",
"re",
".",
"IGNORECASE",
")",
"if",
"not",... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | parse_options | Parse argument options. | bootstrap_py/commands.py | def parse_options(metadata):
"""Parse argument options."""
parser = argparse.ArgumentParser(description='%(prog)s usage:',
prog=__prog__)
setoption(parser, metadata=metadata)
return parser | def parse_options(metadata):
"""Parse argument options."""
parser = argparse.ArgumentParser(description='%(prog)s usage:',
prog=__prog__)
setoption(parser, metadata=metadata)
return parser | [
"Parse",
"argument",
"options",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L72-L77 | [
"def",
"parse_options",
"(",
"metadata",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"description",
"=",
"'%(prog)s usage:'",
",",
"prog",
"=",
"__prog__",
")",
"setoption",
"(",
"parser",
",",
"metadata",
"=",
"metadata",
")",
"return",
... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | main | Execute main processes. | bootstrap_py/commands.py | def main():
"""Execute main processes."""
try:
pkg_version = Update()
if pkg_version.updatable():
pkg_version.show_message()
metadata = control.retreive_metadata()
parser = parse_options(metadata)
argvs = sys.argv
if len(argvs) <= 1:
parser... | def main():
"""Execute main processes."""
try:
pkg_version = Update()
if pkg_version.updatable():
pkg_version.show_message()
metadata = control.retreive_metadata()
parser = parse_options(metadata)
argvs = sys.argv
if len(argvs) <= 1:
parser... | [
"Execute",
"main",
"processes",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L80-L99 | [
"def",
"main",
"(",
")",
":",
"try",
":",
"pkg_version",
"=",
"Update",
"(",
")",
"if",
"pkg_version",
".",
"updatable",
"(",
")",
":",
"pkg_version",
".",
"show_message",
"(",
")",
"metadata",
"=",
"control",
".",
"retreive_metadata",
"(",
")",
"parser"... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | PackageData._set_param | Set name:value property to Package object. | bootstrap_py/package.py | def _set_param(self, name, value):
"""Set name:value property to Package object."""
if name == 'status':
setattr(self, name, self.metadata.status().get(value))
elif name == 'license':
setattr(self, name, self.metadata.licenses().get(value))
elif name == 'name':
... | def _set_param(self, name, value):
"""Set name:value property to Package object."""
if name == 'status':
setattr(self, name, self.metadata.status().get(value))
elif name == 'license':
setattr(self, name, self.metadata.licenses().get(value))
elif name == 'name':
... | [
"Set",
"name",
":",
"value",
"property",
"to",
"Package",
"object",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L32-L42 | [
"def",
"_set_param",
"(",
"self",
",",
"name",
",",
"value",
")",
":",
"if",
"name",
"==",
"'status'",
":",
"setattr",
"(",
"self",
",",
"name",
",",
"self",
".",
"metadata",
".",
"status",
"(",
")",
".",
"get",
"(",
"value",
")",
")",
"elif",
"n... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | PackageData._check_or_set_default_params | Check key and set default vaule when it does not exists. | bootstrap_py/package.py | def _check_or_set_default_params(self):
"""Check key and set default vaule when it does not exists."""
if not hasattr(self, 'date'):
self._set_param('date', datetime.utcnow().strftime('%Y-%m-%d'))
if not hasattr(self, 'version'):
self._set_param('version', self.default_ve... | def _check_or_set_default_params(self):
"""Check key and set default vaule when it does not exists."""
if not hasattr(self, 'date'):
self._set_param('date', datetime.utcnow().strftime('%Y-%m-%d'))
if not hasattr(self, 'version'):
self._set_param('version', self.default_ve... | [
"Check",
"key",
"and",
"set",
"default",
"vaule",
"when",
"it",
"does",
"not",
"exists",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L44-L52 | [
"def",
"_check_or_set_default_params",
"(",
"self",
")",
":",
"if",
"not",
"hasattr",
"(",
"self",
",",
"'date'",
")",
":",
"self",
".",
"_set_param",
"(",
"'date'",
",",
"datetime",
".",
"utcnow",
"(",
")",
".",
"strftime",
"(",
"'%Y-%m-%d'",
")",
")",
... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | PackageTree.move | Move directory from working directory to output directory. | bootstrap_py/package.py | def move(self):
"""Move directory from working directory to output directory."""
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
shutil.move(self.tmpdir, os.path.join(self.outdir, self.name)) | def move(self):
"""Move directory from working directory to output directory."""
if not os.path.isdir(self.outdir):
os.makedirs(self.outdir)
shutil.move(self.tmpdir, os.path.join(self.outdir, self.name)) | [
"Move",
"directory",
"from",
"working",
"directory",
"to",
"output",
"directory",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L169-L173 | [
"def",
"move",
"(",
"self",
")",
":",
"if",
"not",
"os",
".",
"path",
".",
"isdir",
"(",
"self",
".",
"outdir",
")",
":",
"os",
".",
"makedirs",
"(",
"self",
".",
"outdir",
")",
"shutil",
".",
"move",
"(",
"self",
".",
"tmpdir",
",",
"os",
".",... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | PackageTree.vcs_init | Initialize VCS repository. | bootstrap_py/package.py | def vcs_init(self):
"""Initialize VCS repository."""
VCS(os.path.join(self.outdir, self.name), self.pkg_data) | def vcs_init(self):
"""Initialize VCS repository."""
VCS(os.path.join(self.outdir, self.name), self.pkg_data) | [
"Initialize",
"VCS",
"repository",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L185-L187 | [
"def",
"vcs_init",
"(",
"self",
")",
":",
"VCS",
"(",
"os",
".",
"path",
".",
"join",
"(",
"self",
".",
"outdir",
",",
"self",
".",
"name",
")",
",",
"self",
".",
"pkg_data",
")"
] | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | example_capture | example_capture
An example capture script
Change the network interface by ``export CAP_DEVICE=eth0`` | network_pipeline/scripts/base_capture.py | def example_capture():
"""example_capture
An example capture script
Change the network interface by ``export CAP_DEVICE=eth0``
"""
dev = ev(
"CAP_DEVICE",
"lo")
"""
Ignore ports for forwarding to consolidators:
Redis Internal VM: 6379, 16379
RabbitMQ Internal VM... | def example_capture():
"""example_capture
An example capture script
Change the network interface by ``export CAP_DEVICE=eth0``
"""
dev = ev(
"CAP_DEVICE",
"lo")
"""
Ignore ports for forwarding to consolidators:
Redis Internal VM: 6379, 16379
RabbitMQ Internal VM... | [
"example_capture"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/base_capture.py#L13-L48 | [
"def",
"example_capture",
"(",
")",
":",
"dev",
"=",
"ev",
"(",
"\"CAP_DEVICE\"",
",",
"\"lo\"",
")",
"\"\"\"\n Ignore ports for forwarding to consolidators:\n\n Redis Internal VM: 6379, 16379\n RabbitMQ Internal VM: 5672, 15672, 25672\n \"\"\"",
"# http://biot.com/capstats/b... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | capture_udp_packets | capture_udp_packets
Capture ``UDP`` packets and call the ``handle_packets`` method
Change the network interface by ``export CAP_DEVICE=eth0`` | network_pipeline/scripts/capture_udp.py | def capture_udp_packets():
"""capture_udp_packets
Capture ``UDP`` packets and call the ``handle_packets`` method
Change the network interface by ``export CAP_DEVICE=eth0``
"""
dev = ev(
"CAP_DEVICE",
"lo")
"""
Ignore ports for forwarding to consolidators:
Redis VM: 6... | def capture_udp_packets():
"""capture_udp_packets
Capture ``UDP`` packets and call the ``handle_packets`` method
Change the network interface by ``export CAP_DEVICE=eth0``
"""
dev = ev(
"CAP_DEVICE",
"lo")
"""
Ignore ports for forwarding to consolidators:
Redis VM: 6... | [
"capture_udp_packets"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/capture_udp.py#L13-L48 | [
"def",
"capture_udp_packets",
"(",
")",
":",
"dev",
"=",
"ev",
"(",
"\"CAP_DEVICE\"",
",",
"\"lo\"",
")",
"\"\"\"\n Ignore ports for forwarding to consolidators:\n\n Redis VM: 6379, 16379\n RabbitMQ VM: 5672, 15672, 25672\n\n \"\"\"",
"# http://biot.com/capstats/bpf.html",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | find_steam_location | Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
Steam is not installed. | pysteam/winutils.py | def find_steam_location():
"""
Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
Steam is not installed.
"""
if registry is None:
return None
key = registry.CreateKey(registry.HKEY_CURRENT_USER,"Software\... | def find_steam_location():
"""
Finds the location of the current Steam installation on Windows machines.
Returns None for any non-Windows machines, or for Windows machines where
Steam is not installed.
"""
if registry is None:
return None
key = registry.CreateKey(registry.HKEY_CURRENT_USER,"Software\... | [
"Finds",
"the",
"location",
"of",
"the",
"current",
"Steam",
"installation",
"on",
"Windows",
"machines",
".",
"Returns",
"None",
"for",
"any",
"non",
"-",
"Windows",
"machines",
"or",
"for",
"Windows",
"machines",
"where",
"Steam",
"is",
"not",
"installed",
... | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/winutils.py#L10-L20 | [
"def",
"find_steam_location",
"(",
")",
":",
"if",
"registry",
"is",
"None",
":",
"return",
"None",
"key",
"=",
"registry",
".",
"CreateKey",
"(",
"registry",
".",
"HKEY_CURRENT_USER",
",",
"\"Software\\Valve\\Steam\"",
")",
"return",
"registry",
".",
"QueryValu... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | convert_pkt_to_json | convert_pkt_to_json
Inspired by:
https://gist.githubusercontent.com/cr0hn/1b0c2e672cd0721d3a07/raw/9144676ceb12dbd545e6dce366822bbedde8de2c/pkg_to_json.py
This function convert a Scapy packet to JSON
:param pkg: A kamene package
:type pkg: objects
:return: A JSON data
:rtype: dict() | network_pipeline/convert_pkt_to_json.py | def convert_pkt_to_json(pkg):
""" convert_pkt_to_json
Inspired by:
https://gist.githubusercontent.com/cr0hn/1b0c2e672cd0721d3a07/raw/9144676ceb12dbd545e6dce366822bbedde8de2c/pkg_to_json.py
This function convert a Scapy packet to JSON
:param pkg: A kamene package
:type pkg: objects
:return:... | def convert_pkt_to_json(pkg):
""" convert_pkt_to_json
Inspired by:
https://gist.githubusercontent.com/cr0hn/1b0c2e672cd0721d3a07/raw/9144676ceb12dbd545e6dce366822bbedde8de2c/pkg_to_json.py
This function convert a Scapy packet to JSON
:param pkg: A kamene package
:type pkg: objects
:return:... | [
"convert_pkt_to_json",
"Inspired",
"by",
":",
"https",
":",
"//",
"gist",
".",
"githubusercontent",
".",
"com",
"/",
"cr0hn",
"/",
"1b0c2e672cd0721d3a07",
"/",
"raw",
"/",
"9144676ceb12dbd545e6dce366822bbedde8de2c",
"/",
"pkg_to_json",
".",
"py",
"This",
"function",... | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/convert_pkt_to_json.py#L12-L259 | [
"def",
"convert_pkt_to_json",
"(",
"pkg",
")",
":",
"results",
"=",
"defaultdict",
"(",
"dict",
")",
"try",
":",
"for",
"index",
"in",
"range",
"(",
"0",
",",
"len",
"(",
"pkg",
")",
")",
":",
"layer",
"=",
"pkg",
"[",
"index",
"]",
"# Get layer name... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | plot_PCoA | Plot PCoA principal coordinates scaled by the relative abundances of
otu_name. | bin/PCoA_bubble.py | def plot_PCoA(cat_data, otu_name, unifrac, names, colors, xr, yr, outDir,
save_as, plot_style):
"""
Plot PCoA principal coordinates scaled by the relative abundances of
otu_name.
"""
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
for i, cat in enumerate(cat_data):... | def plot_PCoA(cat_data, otu_name, unifrac, names, colors, xr, yr, outDir,
save_as, plot_style):
"""
Plot PCoA principal coordinates scaled by the relative abundances of
otu_name.
"""
fig = plt.figure(figsize=(14, 8))
ax = fig.add_subplot(111)
for i, cat in enumerate(cat_data):... | [
"Plot",
"PCoA",
"principal",
"coordinates",
"scaled",
"by",
"the",
"relative",
"abundances",
"of",
"otu_name",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/PCoA_bubble.py#L36-L65 | [
"def",
"plot_PCoA",
"(",
"cat_data",
",",
"otu_name",
",",
"unifrac",
",",
"names",
",",
"colors",
",",
"xr",
",",
"yr",
",",
"outDir",
",",
"save_as",
",",
"plot_style",
")",
":",
"fig",
"=",
"plt",
".",
"figure",
"(",
"figsize",
"=",
"(",
"14",
"... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | split_by_category | Split up the column data in a biom table by mapping category value. | bin/transpose_biom.py | def split_by_category(biom_cols, mapping, category_id):
"""
Split up the column data in a biom table by mapping category value.
"""
columns = defaultdict(list)
for i, col in enumerate(biom_cols):
columns[mapping[col['id']][category_id]].append((i, col))
return columns | def split_by_category(biom_cols, mapping, category_id):
"""
Split up the column data in a biom table by mapping category value.
"""
columns = defaultdict(list)
for i, col in enumerate(biom_cols):
columns[mapping[col['id']][category_id]].append((i, col))
return columns | [
"Split",
"up",
"the",
"column",
"data",
"in",
"a",
"biom",
"table",
"by",
"mapping",
"category",
"value",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/transpose_biom.py#L17-L25 | [
"def",
"split_by_category",
"(",
"biom_cols",
",",
"mapping",
",",
"category_id",
")",
":",
"columns",
"=",
"defaultdict",
"(",
"list",
")",
"for",
"i",
",",
"col",
"in",
"enumerate",
"(",
"biom_cols",
")",
":",
"columns",
"[",
"mapping",
"[",
"col",
"["... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | print_line | print line if starts with ... | ctbBio/stockholm2oneline.py | def print_line(l):
"""
print line if starts with ...
"""
print_lines = ['# STOCKHOLM', '#=GF', '#=GS', ' ']
if len(l.split()) == 0:
return True
for start in print_lines:
if l.startswith(start):
return True
return False | def print_line(l):
"""
print line if starts with ...
"""
print_lines = ['# STOCKHOLM', '#=GF', '#=GS', ' ']
if len(l.split()) == 0:
return True
for start in print_lines:
if l.startswith(start):
return True
return False | [
"print",
"line",
"if",
"starts",
"with",
"..."
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L11-L21 | [
"def",
"print_line",
"(",
"l",
")",
":",
"print_lines",
"=",
"[",
"'# STOCKHOLM'",
",",
"'#=GF'",
",",
"'#=GS'",
",",
"' '",
"]",
"if",
"len",
"(",
"l",
".",
"split",
"(",
")",
")",
"==",
"0",
":",
"return",
"True",
"for",
"start",
"in",
"print_lin... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | stock2one | convert stockholm to single line format | ctbBio/stockholm2oneline.py | def stock2one(stock):
"""
convert stockholm to single line format
"""
lines = {}
for line in stock:
line = line.strip()
if print_line(line) is True:
yield line
continue
if line.startswith('//'):
continue
ID, seq = line.rsplit(' ', 1... | def stock2one(stock):
"""
convert stockholm to single line format
"""
lines = {}
for line in stock:
line = line.strip()
if print_line(line) is True:
yield line
continue
if line.startswith('//'):
continue
ID, seq = line.rsplit(' ', 1... | [
"convert",
"stockholm",
"to",
"single",
"line",
"format"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L23-L44 | [
"def",
"stock2one",
"(",
"stock",
")",
":",
"lines",
"=",
"{",
"}",
"for",
"line",
"in",
"stock",
":",
"line",
"=",
"line",
".",
"strip",
"(",
")",
"if",
"print_line",
"(",
"line",
")",
"is",
"True",
":",
"yield",
"line",
"continue",
"if",
"line",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | math_func | Statics the methods. wut. | uno/helpers.py | def math_func(f):
"""
Statics the methods. wut.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if len(args) > 0:
return_type = type(args[0])
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
re... | def math_func(f):
"""
Statics the methods. wut.
"""
@wraps(f)
def wrapper(*args, **kwargs):
if len(args) > 0:
return_type = type(args[0])
if kwargs.has_key('return_type'):
return_type = kwargs['return_type']
kwargs.pop('return_type')
re... | [
"Statics",
"the",
"methods",
".",
"wut",
"."
] | elbow-jason/Uno-deprecated | python | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/helpers.py#L8-L22 | [
"def",
"math_func",
"(",
"f",
")",
":",
"@",
"wraps",
"(",
"f",
")",
"def",
"wrapper",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"len",
"(",
"args",
")",
">",
"0",
":",
"return_type",
"=",
"type",
"(",
"args",
"[",
"0",
"]",
... | 4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4 |
train | dump_stats | Show stats when pings are done | network_pipeline/scripts/icmp_send_msg.py | def dump_stats(myStats):
"""
Show stats when pings are done
"""
print("\n----%s PYTHON PING Statistics----" % (myStats.thisIP))
if myStats.pktsSent > 0:
myStats.fracLoss = (myStats.pktsSent - myStats.pktsRcvd) \
/ myStats.pktsSent
print(("%d packets transmitted, %d pack... | def dump_stats(myStats):
"""
Show stats when pings are done
"""
print("\n----%s PYTHON PING Statistics----" % (myStats.thisIP))
if myStats.pktsSent > 0:
myStats.fracLoss = (myStats.pktsSent - myStats.pktsRcvd) \
/ myStats.pktsSent
print(("%d packets transmitted, %d pack... | [
"Show",
"stats",
"when",
"pings",
"are",
"done"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/icmp_send_msg.py#L470-L495 | [
"def",
"dump_stats",
"(",
"myStats",
")",
":",
"print",
"(",
"\"\\n----%s PYTHON PING Statistics----\"",
"%",
"(",
"myStats",
".",
"thisIP",
")",
")",
"if",
"myStats",
".",
"pktsSent",
">",
"0",
":",
"myStats",
".",
"fracLoss",
"=",
"(",
"myStats",
".",
"p... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | verbose_ping | Send >count< ping to >destIP< with the given >timeout< and display
the result. | network_pipeline/scripts/icmp_send_msg.py | def verbose_ping(hostname, timeout=WAIT_TIMEOUT, count=NUM_PACKETS,
packet_size=PACKET_SIZE, path_finder=False):
"""
Send >count< ping to >destIP< with the given >timeout< and display
the result.
"""
signal.signal(signal.SIGINT, signal_handler) # Handle Ctrl-C
if hasattr(signa... | def verbose_ping(hostname, timeout=WAIT_TIMEOUT, count=NUM_PACKETS,
packet_size=PACKET_SIZE, path_finder=False):
"""
Send >count< ping to >destIP< with the given >timeout< and display
the result.
"""
signal.signal(signal.SIGINT, signal_handler) # Handle Ctrl-C
if hasattr(signa... | [
"Send",
">",
"count<",
"ping",
"to",
">",
"destIP<",
"with",
"the",
"given",
">",
"timeout<",
"and",
"display",
"the",
"result",
"."
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/scripts/icmp_send_msg.py#L507-L551 | [
"def",
"verbose_ping",
"(",
"hostname",
",",
"timeout",
"=",
"WAIT_TIMEOUT",
",",
"count",
"=",
"NUM_PACKETS",
",",
"packet_size",
"=",
"PACKET_SIZE",
",",
"path_finder",
"=",
"False",
")",
":",
"signal",
".",
"signal",
"(",
"signal",
".",
"SIGINT",
",",
"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | Update.updatable | bootstrap-py package updatable?. | bootstrap_py/update.py | def updatable(self):
"""bootstrap-py package updatable?."""
if self.latest_version > self.current_version:
updatable_version = self.latest_version
else:
updatable_version = False
return updatable_version | def updatable(self):
"""bootstrap-py package updatable?."""
if self.latest_version > self.current_version:
updatable_version = self.latest_version
else:
updatable_version = False
return updatable_version | [
"bootstrap",
"-",
"py",
"package",
"updatable?",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/update.py#L29-L35 | [
"def",
"updatable",
"(",
"self",
")",
":",
"if",
"self",
".",
"latest_version",
">",
"self",
".",
"current_version",
":",
"updatable_version",
"=",
"self",
".",
"latest_version",
"else",
":",
"updatable_version",
"=",
"False",
"return",
"updatable_version"
] | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | Update.show_message | Show message updatable. | bootstrap_py/update.py | def show_message(self):
"""Show message updatable."""
print(
'current version: {current_version}\n'
'latest version : {latest_version}'.format(
current_version=self.current_version,
latest_version=self.latest_version)) | def show_message(self):
"""Show message updatable."""
print(
'current version: {current_version}\n'
'latest version : {latest_version}'.format(
current_version=self.current_version,
latest_version=self.latest_version)) | [
"Show",
"message",
"updatable",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/update.py#L37-L43 | [
"def",
"show_message",
"(",
"self",
")",
":",
"print",
"(",
"'current version: {current_version}\\n'",
"'latest version : {latest_version}'",
".",
"format",
"(",
"current_version",
"=",
"self",
".",
"current_version",
",",
"latest_version",
"=",
"self",
".",
"latest_ver... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | condense_otus | Traverse the input otu-sequence file, collect the non-unique OTU IDs and
file the sequences associated with then under the unique OTU ID as defined
by the input matrix.
:@type otuF: file
:@param otuF: The output file from QIIME's pick_otus.py
:@type nuniqueF: file
:@param nuniqueF: The matrix o... | bin/pick_otus_condense.py | def condense_otus(otuF, nuniqueF):
"""
Traverse the input otu-sequence file, collect the non-unique OTU IDs and
file the sequences associated with then under the unique OTU ID as defined
by the input matrix.
:@type otuF: file
:@param otuF: The output file from QIIME's pick_otus.py
:@type nu... | def condense_otus(otuF, nuniqueF):
"""
Traverse the input otu-sequence file, collect the non-unique OTU IDs and
file the sequences associated with then under the unique OTU ID as defined
by the input matrix.
:@type otuF: file
:@param otuF: The output file from QIIME's pick_otus.py
:@type nu... | [
"Traverse",
"the",
"input",
"otu",
"-",
"sequence",
"file",
"collect",
"the",
"non",
"-",
"unique",
"OTU",
"IDs",
"and",
"file",
"the",
"sequences",
"associated",
"with",
"then",
"under",
"the",
"unique",
"OTU",
"ID",
"as",
"defined",
"by",
"the",
"input",... | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/pick_otus_condense.py#L14-L51 | [
"def",
"condense_otus",
"(",
"otuF",
",",
"nuniqueF",
")",
":",
"uniqueOTUs",
"=",
"set",
"(",
")",
"nuOTUs",
"=",
"{",
"}",
"# parse non-unique otu matrix",
"for",
"line",
"in",
"nuniqueF",
":",
"line",
"=",
"line",
".",
"split",
"(",
")",
"uOTU",
"=",
... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | rna_bases | determine if read overlaps with rna, if so count bases | ctbBio/rRNA_copies.py | def rna_bases(rna_cov, scaffold, bases, line):
"""
determine if read overlaps with rna, if so count bases
"""
start = int(line[3])
stop = start + bases - 1
if scaffold not in rna_cov:
return rna_cov
for pos in rna_cov[scaffold][2]:
ol = get_overlap([start, stop], pos)
... | def rna_bases(rna_cov, scaffold, bases, line):
"""
determine if read overlaps with rna, if so count bases
"""
start = int(line[3])
stop = start + bases - 1
if scaffold not in rna_cov:
return rna_cov
for pos in rna_cov[scaffold][2]:
ol = get_overlap([start, stop], pos)
... | [
"determine",
"if",
"read",
"overlaps",
"with",
"rna",
"if",
"so",
"count",
"bases"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L18-L29 | [
"def",
"rna_bases",
"(",
"rna_cov",
",",
"scaffold",
",",
"bases",
",",
"line",
")",
":",
"start",
"=",
"int",
"(",
"line",
"[",
"3",
"]",
")",
"stop",
"=",
"start",
"+",
"bases",
"-",
"1",
"if",
"scaffold",
"not",
"in",
"rna_cov",
":",
"return",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | parse_s2bins | parse ggKbase scaffold-to-bin mapping
- scaffolds-to-bins and bins-to-scaffolds | ctbBio/rRNA_copies.py | def parse_s2bins(s2bins):
"""
parse ggKbase scaffold-to-bin mapping
- scaffolds-to-bins and bins-to-scaffolds
"""
s2b = {}
b2s = {}
for line in s2bins:
line = line.strip().split()
s, b = line[0], line[1]
if 'UNK' in b:
continue
if len(line) > 2... | def parse_s2bins(s2bins):
"""
parse ggKbase scaffold-to-bin mapping
- scaffolds-to-bins and bins-to-scaffolds
"""
s2b = {}
b2s = {}
for line in s2bins:
line = line.strip().split()
s, b = line[0], line[1]
if 'UNK' in b:
continue
if len(line) > 2... | [
"parse",
"ggKbase",
"scaffold",
"-",
"to",
"-",
"bin",
"mapping",
"-",
"scaffolds",
"-",
"to",
"-",
"bins",
"and",
"bins",
"-",
"to",
"-",
"scaffolds"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L31-L52 | [
"def",
"parse_s2bins",
"(",
"s2bins",
")",
":",
"s2b",
"=",
"{",
"}",
"b2s",
"=",
"{",
"}",
"for",
"line",
"in",
"s2bins",
":",
"line",
"=",
"line",
".",
"strip",
"(",
")",
".",
"split",
"(",
")",
"s",
",",
"b",
"=",
"line",
"[",
"0",
"]",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | parse_rna | parse [16,23]SfromHMM.py output
- rna_cov[scaffold] = [0, 0, []] # [bases, length, ranges] | ctbBio/rRNA_copies.py | def parse_rna(rna, s2bins, min_rna):
"""
parse [16,23]SfromHMM.py output
- rna_cov[scaffold] = [0, 0, []] # [bases, length, ranges]
"""
rna_cov = {}
for seq in parse_fasta(rna):
# check that length passes threshold
length = len(seq[1])
if length < min_rna:
con... | def parse_rna(rna, s2bins, min_rna):
"""
parse [16,23]SfromHMM.py output
- rna_cov[scaffold] = [0, 0, []] # [bases, length, ranges]
"""
rna_cov = {}
for seq in parse_fasta(rna):
# check that length passes threshold
length = len(seq[1])
if length < min_rna:
con... | [
"parse",
"[",
"16",
"23",
"]",
"SfromHMM",
".",
"py",
"output",
"-",
"rna_cov",
"[",
"scaffold",
"]",
"=",
"[",
"0",
"0",
"[]",
"]",
"#",
"[",
"bases",
"length",
"ranges",
"]"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L54-L74 | [
"def",
"parse_rna",
"(",
"rna",
",",
"s2bins",
",",
"min_rna",
")",
":",
"rna_cov",
"=",
"{",
"}",
"for",
"seq",
"in",
"parse_fasta",
"(",
"rna",
")",
":",
"# check that length passes threshold",
"length",
"=",
"len",
"(",
"seq",
"[",
"1",
"]",
")",
"i... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | filter_missing_rna | remove any bins that don't have 16S | ctbBio/rRNA_copies.py | def filter_missing_rna(s2bins, bins2s, rna_cov):
"""
remove any bins that don't have 16S
"""
for bin, scaffolds in list(bins2s.items()):
c = 0
for s in scaffolds:
if s in rna_cov:
c += 1
if c == 0:
del bins2s[bin]
for scaffold, bin in l... | def filter_missing_rna(s2bins, bins2s, rna_cov):
"""
remove any bins that don't have 16S
"""
for bin, scaffolds in list(bins2s.items()):
c = 0
for s in scaffolds:
if s in rna_cov:
c += 1
if c == 0:
del bins2s[bin]
for scaffold, bin in l... | [
"remove",
"any",
"bins",
"that",
"don",
"t",
"have",
"16S"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L76-L90 | [
"def",
"filter_missing_rna",
"(",
"s2bins",
",",
"bins2s",
",",
"rna_cov",
")",
":",
"for",
"bin",
",",
"scaffolds",
"in",
"list",
"(",
"bins2s",
".",
"items",
"(",
")",
")",
":",
"c",
"=",
"0",
"for",
"s",
"in",
"scaffolds",
":",
"if",
"s",
"in",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | calc_bin_cov | calculate bin coverage | ctbBio/rRNA_copies.py | def calc_bin_cov(scaffolds, cov):
"""
calculate bin coverage
"""
bases = sum([cov[i][0] for i in scaffolds if i in cov])
length = sum([cov[i][1] for i in scaffolds if i in cov])
if length == 0:
return 0
return float(float(bases)/float(length)) | def calc_bin_cov(scaffolds, cov):
"""
calculate bin coverage
"""
bases = sum([cov[i][0] for i in scaffolds if i in cov])
length = sum([cov[i][1] for i in scaffolds if i in cov])
if length == 0:
return 0
return float(float(bases)/float(length)) | [
"calculate",
"bin",
"coverage"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L92-L100 | [
"def",
"calc_bin_cov",
"(",
"scaffolds",
",",
"cov",
")",
":",
"bases",
"=",
"sum",
"(",
"[",
"cov",
"[",
"i",
"]",
"[",
"0",
"]",
"for",
"i",
"in",
"scaffolds",
"if",
"i",
"in",
"cov",
"]",
")",
"length",
"=",
"sum",
"(",
"[",
"cov",
"[",
"i... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | copies | 1. determine bin coverage
2. determine rRNA gene coverage
3. compare | ctbBio/rRNA_copies.py | def copies(mapping, s2bins, rna, min_rna = 800, mismatches = 0):
"""
1. determine bin coverage
2. determine rRNA gene coverage
3. compare
"""
cov = {} # cov[scaffold] = [bases, length]
s2bins, bins2s = parse_s2bins(s2bins)
rna_cov = parse_rna(rna, s2bins, min_rna)
s2bins, bins2s = fi... | def copies(mapping, s2bins, rna, min_rna = 800, mismatches = 0):
"""
1. determine bin coverage
2. determine rRNA gene coverage
3. compare
"""
cov = {} # cov[scaffold] = [bases, length]
s2bins, bins2s = parse_s2bins(s2bins)
rna_cov = parse_rna(rna, s2bins, min_rna)
s2bins, bins2s = fi... | [
"1",
".",
"determine",
"bin",
"coverage",
"2",
".",
"determine",
"rRNA",
"gene",
"coverage",
"3",
".",
"compare"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_copies.py#L102-L160 | [
"def",
"copies",
"(",
"mapping",
",",
"s2bins",
",",
"rna",
",",
"min_rna",
"=",
"800",
",",
"mismatches",
"=",
"0",
")",
":",
"cov",
"=",
"{",
"}",
"# cov[scaffold] = [bases, length]",
"s2bins",
",",
"bins2s",
"=",
"parse_s2bins",
"(",
"s2bins",
")",
"r... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | TranslationFormSet.clean | Make sure there is at least a translation has been filled in. If a
default language has been specified, make sure that it exists amongst
translations. | multilingual_model/forms.py | def clean(self):
"""
Make sure there is at least a translation has been filled in. If a
default language has been specified, make sure that it exists amongst
translations.
"""
# First make sure the super's clean method is called upon.
super(TranslationFormSet, se... | def clean(self):
"""
Make sure there is at least a translation has been filled in. If a
default language has been specified, make sure that it exists amongst
translations.
"""
# First make sure the super's clean method is called upon.
super(TranslationFormSet, se... | [
"Make",
"sure",
"there",
"is",
"at",
"least",
"a",
"translation",
"has",
"been",
"filled",
"in",
".",
"If",
"a",
"default",
"language",
"has",
"been",
"specified",
"make",
"sure",
"that",
"it",
"exists",
"amongst",
"translations",
"."
] | dokterbob/django-multilingual-model | python | https://github.com/dokterbob/django-multilingual-model/blob/2479b2c3d6f7b697e95aa1e082c8bc8699f1f638/multilingual_model/forms.py#L19-L58 | [
"def",
"clean",
"(",
"self",
")",
":",
"# First make sure the super's clean method is called upon.",
"super",
"(",
"TranslationFormSet",
",",
"self",
")",
".",
"clean",
"(",
")",
"if",
"settings",
".",
"HIDE_LANGUAGE",
":",
"return",
"if",
"len",
"(",
"self",
".... | 2479b2c3d6f7b697e95aa1e082c8bc8699f1f638 |
train | TranslationFormSet._get_default_language | If a default language has been set, and is still available in
`self.available_languages`, return it and remove it from the list.
If not, simply pop the first available language. | multilingual_model/forms.py | def _get_default_language(self):
"""
If a default language has been set, and is still available in
`self.available_languages`, return it and remove it from the list.
If not, simply pop the first available language.
"""
assert hasattr(self, 'available_languages'), \
... | def _get_default_language(self):
"""
If a default language has been set, and is still available in
`self.available_languages`, return it and remove it from the list.
If not, simply pop the first available language.
"""
assert hasattr(self, 'available_languages'), \
... | [
"If",
"a",
"default",
"language",
"has",
"been",
"set",
"and",
"is",
"still",
"available",
"in",
"self",
".",
"available_languages",
"return",
"it",
"and",
"remove",
"it",
"from",
"the",
"list",
"."
] | dokterbob/django-multilingual-model | python | https://github.com/dokterbob/django-multilingual-model/blob/2479b2c3d6f7b697e95aa1e082c8bc8699f1f638/multilingual_model/forms.py#L68-L94 | [
"def",
"_get_default_language",
"(",
"self",
")",
":",
"assert",
"hasattr",
"(",
"self",
",",
"'available_languages'",
")",
",",
"'No available languages have been generated.'",
"assert",
"len",
"(",
"self",
".",
"available_languages",
")",
">",
"0",
",",
"'No avail... | 2479b2c3d6f7b697e95aa1e082c8bc8699f1f638 |
train | TranslationFormSet._construct_form | Construct the form, overriding the initial value for `language_code`. | multilingual_model/forms.py | def _construct_form(self, i, **kwargs):
"""
Construct the form, overriding the initial value for `language_code`.
"""
if not settings.HIDE_LANGUAGE:
self._construct_available_languages()
form = super(TranslationFormSet, self)._construct_form(i, **kwargs)
if ... | def _construct_form(self, i, **kwargs):
"""
Construct the form, overriding the initial value for `language_code`.
"""
if not settings.HIDE_LANGUAGE:
self._construct_available_languages()
form = super(TranslationFormSet, self)._construct_form(i, **kwargs)
if ... | [
"Construct",
"the",
"form",
"overriding",
"the",
"initial",
"value",
"for",
"language_code",
"."
] | dokterbob/django-multilingual-model | python | https://github.com/dokterbob/django-multilingual-model/blob/2479b2c3d6f7b697e95aa1e082c8bc8699f1f638/multilingual_model/forms.py#L96-L128 | [
"def",
"_construct_form",
"(",
"self",
",",
"i",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"not",
"settings",
".",
"HIDE_LANGUAGE",
":",
"self",
".",
"_construct_available_languages",
"(",
")",
"form",
"=",
"super",
"(",
"TranslationFormSet",
",",
"self",
"... | 2479b2c3d6f7b697e95aa1e082c8bc8699f1f638 |
train | filter_by_sample_pct | Split the list of OTUs (and associated sequence ids) into two lists:
those occurring in more than some percentage of samples and those less than
the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [sequence IDs]]}
:type nsamples: int
:param nsamples: The total number of samples in the ... | bin/prune_otus.py | def filter_by_sample_pct(otus, nsamples, pct, phyl_level):
"""
Split the list of OTUs (and associated sequence ids) into two lists:
those occurring in more than some percentage of samples and those less than
the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [sequence IDs]]}
:type... | def filter_by_sample_pct(otus, nsamples, pct, phyl_level):
"""
Split the list of OTUs (and associated sequence ids) into two lists:
those occurring in more than some percentage of samples and those less than
the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [sequence IDs]]}
:type... | [
"Split",
"the",
"list",
"of",
"OTUs",
"(",
"and",
"associated",
"sequence",
"ids",
")",
"into",
"two",
"lists",
":",
"those",
"occurring",
"in",
"more",
"than",
"some",
"percentage",
"of",
"samples",
"and",
"those",
"less",
"than",
"the",
"cutoff",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/prune_otus.py#L18-L63 | [
"def",
"filter_by_sample_pct",
"(",
"otus",
",",
"nsamples",
",",
"pct",
",",
"phyl_level",
")",
":",
"if",
"phyl_level",
"not",
"in",
"[",
"'k'",
",",
"'p'",
",",
"'c'",
",",
"'o'",
",",
"'f'",
",",
"'g'",
",",
"'s'",
"]",
":",
"phyl_level",
"=",
... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | filter_by_sequence_pct | Split the list of OTUs (and associated sequence ids) into two lists:
those occurring associated with more than some percentage of total sequences
and those less than the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [sequence IDs]]}
:type nseqs: int
:param nseqs: The total number of ... | bin/prune_otus.py | def filter_by_sequence_pct(otus, nseqs, pct, phyl_level):
"""
Split the list of OTUs (and associated sequence ids) into two lists:
those occurring associated with more than some percentage of total sequences
and those less than the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [seque... | def filter_by_sequence_pct(otus, nseqs, pct, phyl_level):
"""
Split the list of OTUs (and associated sequence ids) into two lists:
those occurring associated with more than some percentage of total sequences
and those less than the cutoff.
:type otus: dict
:param otus: {otuid: [taxonomy, [seque... | [
"Split",
"the",
"list",
"of",
"OTUs",
"(",
"and",
"associated",
"sequence",
"ids",
")",
"into",
"two",
"lists",
":",
"those",
"occurring",
"associated",
"with",
"more",
"than",
"some",
"percentage",
"of",
"total",
"sequences",
"and",
"those",
"less",
"than",... | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/prune_otus.py#L66-L109 | [
"def",
"filter_by_sequence_pct",
"(",
"otus",
",",
"nseqs",
",",
"pct",
",",
"phyl_level",
")",
":",
"if",
"phyl_level",
"not",
"in",
"[",
"'k'",
",",
"'p'",
",",
"'c'",
",",
"'o'",
",",
"'f'",
",",
"'g'",
",",
"'s'",
"]",
":",
"phyl_level",
"=",
"... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | fq_merge | merge separate fastq files | ctbBio/fastq_merge.py | def fq_merge(R1, R2):
"""
merge separate fastq files
"""
c = itertools.cycle([1, 2, 3, 4])
for r1, r2 in zip(R1, R2):
n = next(c)
if n == 1:
pair = [[], []]
pair[0].append(r1.strip())
pair[1].append(r2.strip())
if n == 4:
yield pair | def fq_merge(R1, R2):
"""
merge separate fastq files
"""
c = itertools.cycle([1, 2, 3, 4])
for r1, r2 in zip(R1, R2):
n = next(c)
if n == 1:
pair = [[], []]
pair[0].append(r1.strip())
pair[1].append(r2.strip())
if n == 4:
yield pair | [
"merge",
"separate",
"fastq",
"files"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/fastq_merge.py#L13-L25 | [
"def",
"fq_merge",
"(",
"R1",
",",
"R2",
")",
":",
"c",
"=",
"itertools",
".",
"cycle",
"(",
"[",
"1",
",",
"2",
",",
"3",
",",
"4",
"]",
")",
"for",
"r1",
",",
"r2",
"in",
"zip",
"(",
"R1",
",",
"R2",
")",
":",
"n",
"=",
"next",
"(",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | Ketama._build_circle | Creates hash ring. | nydus/contrib/ketama.py | def _build_circle(self):
"""
Creates hash ring.
"""
total_weight = 0
for node in self._nodes:
total_weight += self._weights.get(node, 1)
for node in self._nodes:
weight = self._weights.get(node, 1)
ks = math.floor((40 * len(self._... | def _build_circle(self):
"""
Creates hash ring.
"""
total_weight = 0
for node in self._nodes:
total_weight += self._weights.get(node, 1)
for node in self._nodes:
weight = self._weights.get(node, 1)
ks = math.floor((40 * len(self._... | [
"Creates",
"hash",
"ring",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/contrib/ketama.py#L35-L60 | [
"def",
"_build_circle",
"(",
"self",
")",
":",
"total_weight",
"=",
"0",
"for",
"node",
"in",
"self",
".",
"_nodes",
":",
"total_weight",
"+=",
"self",
".",
"_weights",
".",
"get",
"(",
"node",
",",
"1",
")",
"for",
"node",
"in",
"self",
".",
"_nodes... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | Ketama._get_node_pos | Return node position(integer) for a given key. Else return None | nydus/contrib/ketama.py | def _get_node_pos(self, key):
"""
Return node position(integer) for a given key. Else return None
"""
if not self._hashring:
return None
key = self._gen_key(key)
nodes = self._sorted_keys
pos = bisect(nodes, key)
if pos == len(nodes):
... | def _get_node_pos(self, key):
"""
Return node position(integer) for a given key. Else return None
"""
if not self._hashring:
return None
key = self._gen_key(key)
nodes = self._sorted_keys
pos = bisect(nodes, key)
if pos == len(nodes):
... | [
"Return",
"node",
"position",
"(",
"integer",
")",
"for",
"a",
"given",
"key",
".",
"Else",
"return",
"None"
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/contrib/ketama.py#L62-L76 | [
"def",
"_get_node_pos",
"(",
"self",
",",
"key",
")",
":",
"if",
"not",
"self",
".",
"_hashring",
":",
"return",
"None",
"key",
"=",
"self",
".",
"_gen_key",
"(",
"key",
")",
"nodes",
"=",
"self",
".",
"_sorted_keys",
"pos",
"=",
"bisect",
"(",
"node... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | Ketama._gen_key | Return long integer for a given key, that represent it place on
the hash ring. | nydus/contrib/ketama.py | def _gen_key(self, key):
"""
Return long integer for a given key, that represent it place on
the hash ring.
"""
b_key = self._md5_digest(key)
return self._hashi(b_key, lambda x: x) | def _gen_key(self, key):
"""
Return long integer for a given key, that represent it place on
the hash ring.
"""
b_key = self._md5_digest(key)
return self._hashi(b_key, lambda x: x) | [
"Return",
"long",
"integer",
"for",
"a",
"given",
"key",
"that",
"represent",
"it",
"place",
"on",
"the",
"hash",
"ring",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/contrib/ketama.py#L78-L84 | [
"def",
"_gen_key",
"(",
"self",
",",
"key",
")",
":",
"b_key",
"=",
"self",
".",
"_md5_digest",
"(",
"key",
")",
"return",
"self",
".",
"_hashi",
"(",
"b_key",
",",
"lambda",
"x",
":",
"x",
")"
] | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | Ketama.remove_node | Removes node from circle and rebuild it. | nydus/contrib/ketama.py | def remove_node(self, node):
"""
Removes node from circle and rebuild it.
"""
try:
self._nodes.remove(node)
del self._weights[node]
except (KeyError, ValueError):
pass
self._hashring = dict()
self._sorted_keys = []
... | def remove_node(self, node):
"""
Removes node from circle and rebuild it.
"""
try:
self._nodes.remove(node)
del self._weights[node]
except (KeyError, ValueError):
pass
self._hashring = dict()
self._sorted_keys = []
... | [
"Removes",
"node",
"from",
"circle",
"and",
"rebuild",
"it",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/contrib/ketama.py#L95-L107 | [
"def",
"remove_node",
"(",
"self",
",",
"node",
")",
":",
"try",
":",
"self",
".",
"_nodes",
".",
"remove",
"(",
"node",
")",
"del",
"self",
".",
"_weights",
"[",
"node",
"]",
"except",
"(",
"KeyError",
",",
"ValueError",
")",
":",
"pass",
"self",
... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | Ketama.add_node | Adds node to circle and rebuild it. | nydus/contrib/ketama.py | def add_node(self, node, weight=1):
"""
Adds node to circle and rebuild it.
"""
self._nodes.add(node)
self._weights[node] = weight
self._hashring = dict()
self._sorted_keys = []
self._build_circle() | def add_node(self, node, weight=1):
"""
Adds node to circle and rebuild it.
"""
self._nodes.add(node)
self._weights[node] = weight
self._hashring = dict()
self._sorted_keys = []
self._build_circle() | [
"Adds",
"node",
"to",
"circle",
"and",
"rebuild",
"it",
"."
] | disqus/nydus | python | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/contrib/ketama.py#L109-L118 | [
"def",
"add_node",
"(",
"self",
",",
"node",
",",
"weight",
"=",
"1",
")",
":",
"self",
".",
"_nodes",
".",
"add",
"(",
"node",
")",
"self",
".",
"_weights",
"[",
"node",
"]",
"=",
"weight",
"self",
".",
"_hashring",
"=",
"dict",
"(",
")",
"self"... | 9b505840da47a34f758a830c3992fa5dcb7bb7ad |
train | RecordPacketsToCSV.process_ether_frame | process_ether_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: ether frame for packet | network_pipeline/record_packets_to_csv.py | def process_ether_frame(self,
id=None,
msg=None):
"""process_ether_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
... | def process_ether_frame(self,
id=None,
msg=None):
"""process_ether_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
... | [
"process_ether_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L128-L163 | [
"def",
"process_ether_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_ip_frame | process_ip_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: ip frame for packet | network_pipeline/record_packets_to_csv.py | def process_ip_frame(self,
id=None,
msg=None):
"""process_ip_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param ... | def process_ip_frame(self,
id=None,
msg=None):
"""process_ip_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param ... | [
"process_ip_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L166-L201 | [
"def",
"process_ip_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_ipvsix_frame | process_ipvsix_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: ipv6 frame for packet | network_pipeline/record_packets_to_csv.py | def process_ipvsix_frame(self,
id=None,
msg=None):
"""process_ipvsix_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg... | def process_ipvsix_frame(self,
id=None,
msg=None):
"""process_ipvsix_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg... | [
"process_ipvsix_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L204-L239 | [
"def",
"process_ipvsix_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"d... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_tcp_frame | process_tcp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: tcp frame for packet | network_pipeline/record_packets_to_csv.py | def process_tcp_frame(self,
id=None,
msg=None):
"""process_tcp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_tcp_frame(self,
id=None,
msg=None):
"""process_tcp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_tcp_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L242-L277 | [
"def",
"process_tcp_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_udp_frame | process_udp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: udp frame for packet | network_pipeline/record_packets_to_csv.py | def process_udp_frame(self,
id=None,
msg=None):
"""process_udp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_udp_frame(self,
id=None,
msg=None):
"""process_udp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_udp_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L280-L315 | [
"def",
"process_udp_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_dns_frame | process_dns_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: dns frame for packet | network_pipeline/record_packets_to_csv.py | def process_dns_frame(self,
id=None,
msg=None):
"""process_dns_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_dns_frame(self,
id=None,
msg=None):
"""process_dns_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_dns_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L318-L353 | [
"def",
"process_dns_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_icmp_frame | process_icmp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: icmp frame for packet | network_pipeline/record_packets_to_csv.py | def process_icmp_frame(self,
id=None,
msg=None):
"""process_icmp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
... | def process_icmp_frame(self,
id=None,
msg=None):
"""process_icmp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
... | [
"process_icmp_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L356-L391 | [
"def",
"process_icmp_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_arp_frame | process_arp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: arp frame for packet | network_pipeline/record_packets_to_csv.py | def process_arp_frame(self,
id=None,
msg=None):
"""process_arp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_arp_frame(self,
id=None,
msg=None):
"""process_arp_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_arp_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L394-L429 | [
"def",
"process_arp_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_raw_frame | process_raw_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: raw frame for packet | network_pipeline/record_packets_to_csv.py | def process_raw_frame(self,
id=None,
msg=None):
"""process_raw_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_raw_frame(self,
id=None,
msg=None):
"""process_raw_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_raw_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L432-L467 | [
"def",
"process_raw_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.process_pad_frame | process_pad_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:param msg: pad frame for packet | network_pipeline/record_packets_to_csv.py | def process_pad_frame(self,
id=None,
msg=None):
"""process_pad_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | def process_pad_frame(self,
id=None,
msg=None):
"""process_pad_frame
Convert a complex nested json dictionary
to a flattened dictionary and capture
all unique keys for table construction
:param id: key for this msg
:pa... | [
"process_pad_frame"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L470-L505 | [
"def",
"process_pad_frame",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"# normalize into a dataframe",
"df",
"=",
"json_normalize",
"(",
"msg",
")",
"# convert to a flattened dictionary",
"dt",
"=",
"json",
".",
"loads",
"(",
"df",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.build_flat_msg | build_flat_msg
:param id: unique id for this message
:param msg: message dictionary to flatten | network_pipeline/record_packets_to_csv.py | def build_flat_msg(self,
id=None,
msg=None):
"""build_flat_msg
:param id: unique id for this message
:param msg: message dictionary to flatten
"""
flat_msg = {}
if not id:
log.error("Please pass in an id")
... | def build_flat_msg(self,
id=None,
msg=None):
"""build_flat_msg
:param id: unique id for this message
:param msg: message dictionary to flatten
"""
flat_msg = {}
if not id:
log.error("Please pass in an id")
... | [
"build_flat_msg"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L508-L586 | [
"def",
"build_flat_msg",
"(",
"self",
",",
"id",
"=",
"None",
",",
"msg",
"=",
"None",
")",
":",
"flat_msg",
"=",
"{",
"}",
"if",
"not",
"id",
":",
"log",
".",
"error",
"(",
"\"Please pass in an id\"",
")",
"return",
"None",
"if",
"not",
"msg",
":",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.build_all_keys_dict | build_all_keys_dict | network_pipeline/record_packets_to_csv.py | def build_all_keys_dict(self):
"""build_all_keys_dict"""
log.info("finding keys")
for k in self.eth_keys:
ak = "{}".format(k)
if ak not in self.all_keys:
self.all_keys[ak] = k
# end of building all eths
for k in self.ip_keys:
a... | def build_all_keys_dict(self):
"""build_all_keys_dict"""
log.info("finding keys")
for k in self.eth_keys:
ak = "{}".format(k)
if ak not in self.all_keys:
self.all_keys[ak] = k
# end of building all eths
for k in self.ip_keys:
a... | [
"build_all_keys_dict"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L589-L650 | [
"def",
"build_all_keys_dict",
"(",
"self",
")",
":",
"log",
".",
"info",
"(",
"\"finding keys\"",
")",
"for",
"k",
"in",
"self",
".",
"eth_keys",
":",
"ak",
"=",
"\"{}\"",
".",
"format",
"(",
"k",
")",
"if",
"ak",
"not",
"in",
"self",
".",
"all_keys"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.flatten_all | flatten_all | network_pipeline/record_packets_to_csv.py | def flatten_all(self):
"""flatten_all"""
log.info("flattening - START")
self.all_rows = []
for idx, r in enumerate(self.all_flat):
new_row = {"idx": idx}
for k in self.all_keys_list:
if k in r:
new_row[k] = r[k]
... | def flatten_all(self):
"""flatten_all"""
log.info("flattening - START")
self.all_rows = []
for idx, r in enumerate(self.all_flat):
new_row = {"idx": idx}
for k in self.all_keys_list:
if k in r:
new_row[k] = r[k]
... | [
"flatten_all"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L654-L676 | [
"def",
"flatten_all",
"(",
"self",
")",
":",
"log",
".",
"info",
"(",
"\"flattening - START\"",
")",
"self",
".",
"all_rows",
"=",
"[",
"]",
"for",
"idx",
",",
"r",
"in",
"enumerate",
"(",
"self",
".",
"all_flat",
")",
":",
"new_row",
"=",
"{",
"\"id... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.create_json_archive | create_json_archive | network_pipeline/record_packets_to_csv.py | def create_json_archive(self):
"""create_json_archive"""
archive_data = {"packets": self.recv_msgs,
"dataset": self.dataset_name,
"num_packets": len(self.recv_msgs),
"created": rnow()}
self.write_to_file(archive_data,
... | def create_json_archive(self):
"""create_json_archive"""
archive_data = {"packets": self.recv_msgs,
"dataset": self.dataset_name,
"num_packets": len(self.recv_msgs),
"created": rnow()}
self.write_to_file(archive_data,
... | [
"create_json_archive"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L679-L687 | [
"def",
"create_json_archive",
"(",
"self",
")",
":",
"archive_data",
"=",
"{",
"\"packets\"",
":",
"self",
".",
"recv_msgs",
",",
"\"dataset\"",
":",
"self",
".",
"dataset_name",
",",
"\"num_packets\"",
":",
"len",
"(",
"self",
".",
"recv_msgs",
")",
",",
... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.convert_to_df | convert_to_df | network_pipeline/record_packets_to_csv.py | def convert_to_df(self):
"""convert_to_df"""
log.info(("converting={}")
.format(len(self.all_rows)))
if len(self.all_rows) == 0:
return
self.df = pd.DataFrame(self.all_rows).set_index("idx")
if len(self.df) != len(self.all_rows):
log.e... | def convert_to_df(self):
"""convert_to_df"""
log.info(("converting={}")
.format(len(self.all_rows)))
if len(self.all_rows) == 0:
return
self.df = pd.DataFrame(self.all_rows).set_index("idx")
if len(self.df) != len(self.all_rows):
log.e... | [
"convert_to_df"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L691-L709 | [
"def",
"convert_to_df",
"(",
"self",
")",
":",
"log",
".",
"info",
"(",
"(",
"\"converting={}\"",
")",
".",
"format",
"(",
"len",
"(",
"self",
".",
"all_rows",
")",
")",
")",
"if",
"len",
"(",
"self",
".",
"all_rows",
")",
"==",
"0",
":",
"return",... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.write_to_file | write_to_file
:param data_dict:
:param output_file_path: | network_pipeline/record_packets_to_csv.py | def write_to_file(self,
data_dict,
output_file_path):
"""write_to_file
:param data_dict:
:param output_file_path:
"""
log.info("saving={}".format(output_file_path))
with open(output_file_path, "w") as output_file:
... | def write_to_file(self,
data_dict,
output_file_path):
"""write_to_file
:param data_dict:
:param output_file_path:
"""
log.info("saving={}".format(output_file_path))
with open(output_file_path, "w") as output_file:
... | [
"write_to_file"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L713-L724 | [
"def",
"write_to_file",
"(",
"self",
",",
"data_dict",
",",
"output_file_path",
")",
":",
"log",
".",
"info",
"(",
"\"saving={}\"",
".",
"format",
"(",
"output_file_path",
")",
")",
"with",
"open",
"(",
"output_file_path",
",",
"\"w\"",
")",
"as",
"output_fi... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.save_df_as_csv | save_df_as_csv | network_pipeline/record_packets_to_csv.py | def save_df_as_csv(self):
"""save_df_as_csv"""
if len(self.all_rows) == 0:
log.info(("no df={} to save")
.format(self.df))
return
else:
log.info(("saving "
"packets={} file={} rows={}")
.format(... | def save_df_as_csv(self):
"""save_df_as_csv"""
if len(self.all_rows) == 0:
log.info(("no df={} to save")
.format(self.df))
return
else:
log.info(("saving "
"packets={} file={} rows={}")
.format(... | [
"save_df_as_csv"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L727-L748 | [
"def",
"save_df_as_csv",
"(",
"self",
")",
":",
"if",
"len",
"(",
"self",
".",
"all_rows",
")",
"==",
"0",
":",
"log",
".",
"info",
"(",
"(",
"\"no df={} to save\"",
")",
".",
"format",
"(",
"self",
".",
"df",
")",
")",
"return",
"else",
":",
"log"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.save_data | save_data | network_pipeline/record_packets_to_csv.py | def save_data(self):
"""save_data"""
state = ""
try:
state = "create_json_archive"
log.info("creating json archive")
self.create_json_archive()
state = "building_unique_keys"
log.info("processing all unique keys")
self.bu... | def save_data(self):
"""save_data"""
state = ""
try:
state = "create_json_archive"
log.info("creating json archive")
self.create_json_archive()
state = "building_unique_keys"
log.info("processing all unique keys")
self.bu... | [
"save_data"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L752-L790 | [
"def",
"save_data",
"(",
"self",
")",
":",
"state",
"=",
"\"\"",
"try",
":",
"state",
"=",
"\"create_json_archive\"",
"log",
".",
"info",
"(",
"\"creating json archive\"",
")",
"self",
".",
"create_json_archive",
"(",
")",
"state",
"=",
"\"building_unique_keys\"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.handle_msg | handle_msg
:param body: dictionary contents from the message body
:param org_message: message object can ack, requeue or reject | network_pipeline/record_packets_to_csv.py | def handle_msg(self,
body,
org_message):
"""handle_msg
:param body: dictionary contents from the message body
:param org_message: message object can ack, requeue or reject
"""
if os.path.exists(self.stop_for_file):
log.info(("De... | def handle_msg(self,
body,
org_message):
"""handle_msg
:param body: dictionary contents from the message body
:param org_message: message object can ack, requeue or reject
"""
if os.path.exists(self.stop_for_file):
log.info(("De... | [
"handle_msg"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L793-L879 | [
"def",
"handle_msg",
"(",
"self",
",",
"body",
",",
"org_message",
")",
":",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"self",
".",
"stop_for_file",
")",
":",
"log",
".",
"info",
"(",
"(",
"\"Detected stop_file={} \"",
"\"shutting down\"",
")",
".",
"... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | RecordPacketsToCSV.publish_predictions_to_core | publish_predictions_to_core | network_pipeline/record_packets_to_csv.py | def publish_predictions_to_core(self):
"""publish_predictions_to_core"""
status = FAILED
msg = "not started"
try:
msg = "generating request"
log.info(msg)
# noqa https://stackoverflow.com/questions/29815129/pandas-dataframe-to-list-of-dictionaries
... | def publish_predictions_to_core(self):
"""publish_predictions_to_core"""
status = FAILED
msg = "not started"
try:
msg = "generating request"
log.info(msg)
# noqa https://stackoverflow.com/questions/29815129/pandas-dataframe-to-list-of-dictionaries
... | [
"publish_predictions_to_core"
] | jay-johnson/network-pipeline | python | https://github.com/jay-johnson/network-pipeline/blob/4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa/network_pipeline/record_packets_to_csv.py#L882-L948 | [
"def",
"publish_predictions_to_core",
"(",
"self",
")",
":",
"status",
"=",
"FAILED",
"msg",
"=",
"\"not started\"",
"try",
":",
"msg",
"=",
"\"generating request\"",
"log",
".",
"info",
"(",
"msg",
")",
"# noqa https://stackoverflow.com/questions/29815129/pandas-datafr... | 4e53ae13fe12085e0cf2e5e1aff947368f4f1ffa |
train | FgdcParser._init_data_map | OVERRIDDEN: Initialize required FGDC data map with XPATHS and specialized functions | gis_metadata/fgdc_metadata_parser.py | def _init_data_map(self):
""" OVERRIDDEN: Initialize required FGDC data map with XPATHS and specialized functions """
if self._data_map is not None:
return # Initiation happens once
# Parse and validate the FGDC metadata root
if self._xml_tree is None:
fgdc_ro... | def _init_data_map(self):
""" OVERRIDDEN: Initialize required FGDC data map with XPATHS and specialized functions """
if self._data_map is not None:
return # Initiation happens once
# Parse and validate the FGDC metadata root
if self._xml_tree is None:
fgdc_ro... | [
"OVERRIDDEN",
":",
"Initialize",
"required",
"FGDC",
"data",
"map",
"with",
"XPATHS",
"and",
"specialized",
"functions"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/fgdc_metadata_parser.py#L108-L243 | [
"def",
"_init_data_map",
"(",
"self",
")",
":",
"if",
"self",
".",
"_data_map",
"is",
"not",
"None",
":",
"return",
"# Initiation happens once",
"# Parse and validate the FGDC metadata root",
"if",
"self",
".",
"_xml_tree",
"is",
"None",
":",
"fgdc_root",
"=",
"FG... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | FgdcParser._update_raster_info | Ensures complete removal of raster_info given the two roots: <spdoinfo> and <spref> | gis_metadata/fgdc_metadata_parser.py | def _update_raster_info(self, **update_props):
""" Ensures complete removal of raster_info given the two roots: <spdoinfo> and <spref> """
xpath_map = self._data_structures[update_props['prop']]
return [
update_complex(xpath_root=self._data_map.get('_raster_info_root'), xpath_map=x... | def _update_raster_info(self, **update_props):
""" Ensures complete removal of raster_info given the two roots: <spdoinfo> and <spref> """
xpath_map = self._data_structures[update_props['prop']]
return [
update_complex(xpath_root=self._data_map.get('_raster_info_root'), xpath_map=x... | [
"Ensures",
"complete",
"removal",
"of",
"raster_info",
"given",
"the",
"two",
"roots",
":",
"<spdoinfo",
">",
"and",
"<spref",
">"
] | consbio/gis-metadata-parser | python | https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/fgdc_metadata_parser.py#L266-L274 | [
"def",
"_update_raster_info",
"(",
"self",
",",
"*",
"*",
"update_props",
")",
":",
"xpath_map",
"=",
"self",
".",
"_data_structures",
"[",
"update_props",
"[",
"'prop'",
"]",
"]",
"return",
"[",
"update_complex",
"(",
"xpath_root",
"=",
"self",
".",
"_data_... | 59eefb2e51cd4d8cc3e94623a2167499ca9ef70f |
train | has_custom_image | Returns True if there exists a custom image for app_id. | pysteam/grid.py | def has_custom_image(user_context, app_id):
"""Returns True if there exists a custom image for app_id."""
possible_paths = _valid_custom_image_paths(user_context, app_id)
return any(map(os.path.exists, possible_paths)) | def has_custom_image(user_context, app_id):
"""Returns True if there exists a custom image for app_id."""
possible_paths = _valid_custom_image_paths(user_context, app_id)
return any(map(os.path.exists, possible_paths)) | [
"Returns",
"True",
"if",
"there",
"exists",
"a",
"custom",
"image",
"for",
"app_id",
"."
] | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/grid.py#L32-L35 | [
"def",
"has_custom_image",
"(",
"user_context",
",",
"app_id",
")",
":",
"possible_paths",
"=",
"_valid_custom_image_paths",
"(",
"user_context",
",",
"app_id",
")",
"return",
"any",
"(",
"map",
"(",
"os",
".",
"path",
".",
"exists",
",",
"possible_paths",
")"... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | get_custom_image | Returns the custom image associated with a given app. If there are
multiple candidate images on disk, one is chosen arbitrarily. | pysteam/grid.py | def get_custom_image(user_context, app_id):
"""Returns the custom image associated with a given app. If there are
multiple candidate images on disk, one is chosen arbitrarily."""
possible_paths = _valid_custom_image_paths(user_context, app_id)
existing_images = filter(os.path.exists, possible_paths)
if len(ex... | def get_custom_image(user_context, app_id):
"""Returns the custom image associated with a given app. If there are
multiple candidate images on disk, one is chosen arbitrarily."""
possible_paths = _valid_custom_image_paths(user_context, app_id)
existing_images = filter(os.path.exists, possible_paths)
if len(ex... | [
"Returns",
"the",
"custom",
"image",
"associated",
"with",
"a",
"given",
"app",
".",
"If",
"there",
"are",
"multiple",
"candidate",
"images",
"on",
"disk",
"one",
"is",
"chosen",
"arbitrarily",
"."
] | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/grid.py#L37-L43 | [
"def",
"get_custom_image",
"(",
"user_context",
",",
"app_id",
")",
":",
"possible_paths",
"=",
"_valid_custom_image_paths",
"(",
"user_context",
",",
"app_id",
")",
"existing_images",
"=",
"filter",
"(",
"os",
".",
"path",
".",
"exists",
",",
"possible_paths",
... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | set_custom_image | Sets the custom image for `app_id` to be the image located at
`image_path`. If there already exists a custom image for `app_id` it will
be deleted. Returns True is setting the image was successful. | pysteam/grid.py | def set_custom_image(user_context, app_id, image_path):
"""Sets the custom image for `app_id` to be the image located at
`image_path`. If there already exists a custom image for `app_id` it will
be deleted. Returns True is setting the image was successful."""
if image_path is None:
return False
if not os... | def set_custom_image(user_context, app_id, image_path):
"""Sets the custom image for `app_id` to be the image located at
`image_path`. If there already exists a custom image for `app_id` it will
be deleted. Returns True is setting the image was successful."""
if image_path is None:
return False
if not os... | [
"Sets",
"the",
"custom",
"image",
"for",
"app_id",
"to",
"be",
"the",
"image",
"located",
"at",
"image_path",
".",
"If",
"there",
"already",
"exists",
"a",
"custom",
"image",
"for",
"app_id",
"it",
"will",
"be",
"deleted",
".",
"Returns",
"True",
"is",
"... | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/grid.py#L45-L70 | [
"def",
"set_custom_image",
"(",
"user_context",
",",
"app_id",
",",
"image_path",
")",
":",
"if",
"image_path",
"is",
"None",
":",
"return",
"False",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"image_path",
")",
":",
"return",
"False",
"(",
"roo... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | Profile.from_file | Read an orthography profile from a metadata file or a default tab-separated profile file. | src/segments/profile.py | def from_file(cls, fname, form=None):
"""
Read an orthography profile from a metadata file or a default tab-separated profile file.
"""
try:
tg = TableGroup.from_file(fname)
opfname = None
except JSONDecodeError:
tg = TableGroup.fromvalue(cls.M... | def from_file(cls, fname, form=None):
"""
Read an orthography profile from a metadata file or a default tab-separated profile file.
"""
try:
tg = TableGroup.from_file(fname)
opfname = None
except JSONDecodeError:
tg = TableGroup.fromvalue(cls.M... | [
"Read",
"an",
"orthography",
"profile",
"from",
"a",
"metadata",
"file",
"or",
"a",
"default",
"tab",
"-",
"separated",
"profile",
"file",
"."
] | cldf/segments | python | https://github.com/cldf/segments/blob/9136a4ec89555bf9b574399ffbb07f3cc9a9f45f/src/segments/profile.py#L100-L117 | [
"def",
"from_file",
"(",
"cls",
",",
"fname",
",",
"form",
"=",
"None",
")",
":",
"try",
":",
"tg",
"=",
"TableGroup",
".",
"from_file",
"(",
"fname",
")",
"opfname",
"=",
"None",
"except",
"JSONDecodeError",
":",
"tg",
"=",
"TableGroup",
".",
"fromval... | 9136a4ec89555bf9b574399ffbb07f3cc9a9f45f |
train | Profile.from_text | Create a Profile instance from the Unicode graphemes found in `text`.
Parameters
----------
text
mapping
Returns
-------
A Profile instance. | src/segments/profile.py | def from_text(cls, text, mapping='mapping'):
"""
Create a Profile instance from the Unicode graphemes found in `text`.
Parameters
----------
text
mapping
Returns
-------
A Profile instance.
"""
graphemes = Counter(grapheme_patter... | def from_text(cls, text, mapping='mapping'):
"""
Create a Profile instance from the Unicode graphemes found in `text`.
Parameters
----------
text
mapping
Returns
-------
A Profile instance.
"""
graphemes = Counter(grapheme_patter... | [
"Create",
"a",
"Profile",
"instance",
"from",
"the",
"Unicode",
"graphemes",
"found",
"in",
"text",
"."
] | cldf/segments | python | https://github.com/cldf/segments/blob/9136a4ec89555bf9b574399ffbb07f3cc9a9f45f/src/segments/profile.py#L120-L141 | [
"def",
"from_text",
"(",
"cls",
",",
"text",
",",
"mapping",
"=",
"'mapping'",
")",
":",
"graphemes",
"=",
"Counter",
"(",
"grapheme_pattern",
".",
"findall",
"(",
"text",
")",
")",
"specs",
"=",
"[",
"OrderedDict",
"(",
"[",
"(",
"cls",
".",
"GRAPHEME... | 9136a4ec89555bf9b574399ffbb07f3cc9a9f45f |
train | split_fasta | split fasta file into separate fasta files based on list of scaffolds
that belong to each separate file | ctbBio/name2fasta.py | def split_fasta(f, id2f):
"""
split fasta file into separate fasta files based on list of scaffolds
that belong to each separate file
"""
opened = {}
for seq in parse_fasta(f):
id = seq[0].split('>')[1].split()[0]
if id not in id2f:
continue
fasta = id2f[id]
... | def split_fasta(f, id2f):
"""
split fasta file into separate fasta files based on list of scaffolds
that belong to each separate file
"""
opened = {}
for seq in parse_fasta(f):
id = seq[0].split('>')[1].split()[0]
if id not in id2f:
continue
fasta = id2f[id]
... | [
"split",
"fasta",
"file",
"into",
"separate",
"fasta",
"files",
"based",
"on",
"list",
"of",
"scaffolds",
"that",
"belong",
"to",
"each",
"separate",
"file"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/name2fasta.py#L7-L22 | [
"def",
"split_fasta",
"(",
"f",
",",
"id2f",
")",
":",
"opened",
"=",
"{",
"}",
"for",
"seq",
"in",
"parse_fasta",
"(",
"f",
")",
":",
"id",
"=",
"seq",
"[",
"0",
"]",
".",
"split",
"(",
"'>'",
")",
"[",
"1",
"]",
".",
"split",
"(",
")",
"[... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | Steam._is_user_directory | Check whether `pathname` is a valid user data directory
This method is meant to be called on the contents of the userdata dir.
As such, it will return True when `pathname` refers to a directory name
that can be interpreted as a users' userID. | pysteam/legacy/steam.py | def _is_user_directory(self, pathname):
"""Check whether `pathname` is a valid user data directory
This method is meant to be called on the contents of the userdata dir.
As such, it will return True when `pathname` refers to a directory name
that can be interpreted as a users' userID.
"""... | def _is_user_directory(self, pathname):
"""Check whether `pathname` is a valid user data directory
This method is meant to be called on the contents of the userdata dir.
As such, it will return True when `pathname` refers to a directory name
that can be interpreted as a users' userID.
"""... | [
"Check",
"whether",
"pathname",
"is",
"a",
"valid",
"user",
"data",
"directory"
] | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/legacy/steam.py#L47-L58 | [
"def",
"_is_user_directory",
"(",
"self",
",",
"pathname",
")",
":",
"fullpath",
"=",
"os",
".",
"path",
".",
"join",
"(",
"self",
".",
"userdata_location",
"(",
")",
",",
"pathname",
")",
"# SteamOS puts a directory named 'anonymous' in the userdata directory",
"# ... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | Steam.local_users | Returns an array of user ids for users on the filesystem | pysteam/legacy/steam.py | def local_users(self):
"""Returns an array of user ids for users on the filesystem"""
# Any users on the machine will have an entry inside of the userdata
# folder. As such, the easiest way to find a list of all users on the
# machine is to just list the folders inside userdata
u... | def local_users(self):
"""Returns an array of user ids for users on the filesystem"""
# Any users on the machine will have an entry inside of the userdata
# folder. As such, the easiest way to find a list of all users on the
# machine is to just list the folders inside userdata
u... | [
"Returns",
"an",
"array",
"of",
"user",
"ids",
"for",
"users",
"on",
"the",
"filesystem"
] | scottrice/pysteam | python | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/legacy/steam.py#L80-L87 | [
"def",
"local_users",
"(",
"self",
")",
":",
"# Any users on the machine will have an entry inside of the userdata",
"# folder. As such, the easiest way to find a list of all users on the",
"# machine is to just list the folders inside userdata",
"userdirs",
"=",
"filter",
"(",
"self",
"... | 1eb2254b5235a053a953e596fa7602d0b110245d |
train | calculate_temperature_equivalent | Calculates the temperature equivalent from a series of average daily temperatures
according to the formula: 0.6 * tempDay0 + 0.3 * tempDay-1 + 0.1 * tempDay-2
Parameters
----------
series : Pandas Series
Returns
-------
Pandas Series | opengrid/library/weather.py | def calculate_temperature_equivalent(temperatures):
"""
Calculates the temperature equivalent from a series of average daily temperatures
according to the formula: 0.6 * tempDay0 + 0.3 * tempDay-1 + 0.1 * tempDay-2
Parameters
----------
series : Pandas Series
Returns
-------
Pandas... | def calculate_temperature_equivalent(temperatures):
"""
Calculates the temperature equivalent from a series of average daily temperatures
according to the formula: 0.6 * tempDay0 + 0.3 * tempDay-1 + 0.1 * tempDay-2
Parameters
----------
series : Pandas Series
Returns
-------
Pandas... | [
"Calculates",
"the",
"temperature",
"equivalent",
"from",
"a",
"series",
"of",
"average",
"daily",
"temperatures",
"according",
"to",
"the",
"formula",
":",
"0",
".",
"6",
"*",
"tempDay0",
"+",
"0",
".",
"3",
"*",
"tempDay",
"-",
"1",
"+",
"0",
".",
"1... | opengridcc/opengrid | python | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/weather.py#L12-L28 | [
"def",
"calculate_temperature_equivalent",
"(",
"temperatures",
")",
":",
"ret",
"=",
"0.6",
"*",
"temperatures",
"+",
"0.3",
"*",
"temperatures",
".",
"shift",
"(",
"1",
")",
"+",
"0.1",
"*",
"temperatures",
".",
"shift",
"(",
"2",
")",
"ret",
".",
"nam... | 69b8da3c8fcea9300226c45ef0628cd6d4307651 |
train | _calculate_degree_days | Calculates degree days, starting with a series of temperature equivalent values
Parameters
----------
temperature_equivalent : Pandas Series
base_temperature : float
cooling : bool
Set True if you want cooling degree days instead of heating degree days
Returns
-------
Pandas Se... | opengrid/library/weather.py | def _calculate_degree_days(temperature_equivalent, base_temperature, cooling=False):
"""
Calculates degree days, starting with a series of temperature equivalent values
Parameters
----------
temperature_equivalent : Pandas Series
base_temperature : float
cooling : bool
Set True if y... | def _calculate_degree_days(temperature_equivalent, base_temperature, cooling=False):
"""
Calculates degree days, starting with a series of temperature equivalent values
Parameters
----------
temperature_equivalent : Pandas Series
base_temperature : float
cooling : bool
Set True if y... | [
"Calculates",
"degree",
"days",
"starting",
"with",
"a",
"series",
"of",
"temperature",
"equivalent",
"values"
] | opengridcc/opengrid | python | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/weather.py#L31-L59 | [
"def",
"_calculate_degree_days",
"(",
"temperature_equivalent",
",",
"base_temperature",
",",
"cooling",
"=",
"False",
")",
":",
"if",
"cooling",
":",
"ret",
"=",
"temperature_equivalent",
"-",
"base_temperature",
"else",
":",
"ret",
"=",
"base_temperature",
"-",
... | 69b8da3c8fcea9300226c45ef0628cd6d4307651 |
train | compute_degree_days | Compute degree-days for heating and/or cooling
Parameters
----------
ts : pandas.Series
Contains ambient (outside) temperature. Series name (ts.name) does not matter.
heating_base_temperatures: list
For each base temperature the heating degree-days will be computed
cooling_base_temp... | opengrid/library/weather.py | def compute_degree_days(ts, heating_base_temperatures, cooling_base_temperatures):
"""
Compute degree-days for heating and/or cooling
Parameters
----------
ts : pandas.Series
Contains ambient (outside) temperature. Series name (ts.name) does not matter.
heating_base_temperatures: list
... | def compute_degree_days(ts, heating_base_temperatures, cooling_base_temperatures):
"""
Compute degree-days for heating and/or cooling
Parameters
----------
ts : pandas.Series
Contains ambient (outside) temperature. Series name (ts.name) does not matter.
heating_base_temperatures: list
... | [
"Compute",
"degree",
"-",
"days",
"for",
"heating",
"and",
"/",
"or",
"cooling"
] | opengridcc/opengrid | python | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/weather.py#L62-L96 | [
"def",
"compute_degree_days",
"(",
"ts",
",",
"heating_base_temperatures",
",",
"cooling_base_temperatures",
")",
":",
"# verify the sampling rate: should be at least daily.",
"mean_sampling_rate",
"=",
"(",
"ts",
".",
"index",
"[",
"-",
"1",
"]",
"-",
"ts",
".",
"ind... | 69b8da3c8fcea9300226c45ef0628cd6d4307651 |
train | Classifiers.status | Development status. | bootstrap_py/classifiers.py | def status(self):
"""Development status."""
return {self._acronym_status(l): l for l in self.resp_text.split('\n')
if l.startswith(self.prefix_status)} | def status(self):
"""Development status."""
return {self._acronym_status(l): l for l in self.resp_text.split('\n')
if l.startswith(self.prefix_status)} | [
"Development",
"status",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/classifiers.py#L33-L36 | [
"def",
"status",
"(",
"self",
")",
":",
"return",
"{",
"self",
".",
"_acronym_status",
"(",
"l",
")",
":",
"l",
"for",
"l",
"in",
"self",
".",
"resp_text",
".",
"split",
"(",
"'\\n'",
")",
"if",
"l",
".",
"startswith",
"(",
"self",
".",
"prefix_sta... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | Classifiers.licenses | OSI Approved license. | bootstrap_py/classifiers.py | def licenses(self):
"""OSI Approved license."""
return {self._acronym_lic(l): l for l in self.resp_text.split('\n')
if l.startswith(self.prefix_lic)} | def licenses(self):
"""OSI Approved license."""
return {self._acronym_lic(l): l for l in self.resp_text.split('\n')
if l.startswith(self.prefix_lic)} | [
"OSI",
"Approved",
"license",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/classifiers.py#L43-L46 | [
"def",
"licenses",
"(",
"self",
")",
":",
"return",
"{",
"self",
".",
"_acronym_lic",
"(",
"l",
")",
":",
"l",
"for",
"l",
"in",
"self",
".",
"resp_text",
".",
"split",
"(",
"'\\n'",
")",
"if",
"l",
".",
"startswith",
"(",
"self",
".",
"prefix_lic"... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | Classifiers.licenses_desc | Remove prefix. | bootstrap_py/classifiers.py | def licenses_desc(self):
"""Remove prefix."""
return {self._acronym_lic(l): l.split(self.prefix_lic)[1]
for l in self.resp_text.split('\n')
if l.startswith(self.prefix_lic)} | def licenses_desc(self):
"""Remove prefix."""
return {self._acronym_lic(l): l.split(self.prefix_lic)[1]
for l in self.resp_text.split('\n')
if l.startswith(self.prefix_lic)} | [
"Remove",
"prefix",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/classifiers.py#L48-L52 | [
"def",
"licenses_desc",
"(",
"self",
")",
":",
"return",
"{",
"self",
".",
"_acronym_lic",
"(",
"l",
")",
":",
"l",
".",
"split",
"(",
"self",
".",
"prefix_lic",
")",
"[",
"1",
"]",
"for",
"l",
"in",
"self",
".",
"resp_text",
".",
"split",
"(",
"... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | Classifiers._acronym_lic | Convert license acronym. | bootstrap_py/classifiers.py | def _acronym_lic(self, license_statement):
"""Convert license acronym."""
pat = re.compile(r'\(([\w+\W?\s?]+)\)')
if pat.search(license_statement):
lic = pat.search(license_statement).group(1)
if lic.startswith('CNRI'):
acronym_licence = lic[:4]
... | def _acronym_lic(self, license_statement):
"""Convert license acronym."""
pat = re.compile(r'\(([\w+\W?\s?]+)\)')
if pat.search(license_statement):
lic = pat.search(license_statement).group(1)
if lic.startswith('CNRI'):
acronym_licence = lic[:4]
... | [
"Convert",
"license",
"acronym",
"."
] | mkouhei/bootstrap-py | python | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/classifiers.py#L54-L67 | [
"def",
"_acronym_lic",
"(",
"self",
",",
"license_statement",
")",
":",
"pat",
"=",
"re",
".",
"compile",
"(",
"r'\\(([\\w+\\W?\\s?]+)\\)'",
")",
"if",
"pat",
".",
"search",
"(",
"license_statement",
")",
":",
"lic",
"=",
"pat",
".",
"search",
"(",
"licens... | 95d56ed98ef409fd9f019dc352fd1c3711533275 |
train | calcMD5 | calc MD5 based on path | ctbBio/ncbi_download.py | def calcMD5(path):
"""
calc MD5 based on path
"""
# check that file exists
if os.path.exists(path) is False:
yield False
else:
command = ['md5sum', path]
p = Popen(command, stdout = PIPE)
for line in p.communicate()[0].splitlines():
yield line.decode('... | def calcMD5(path):
"""
calc MD5 based on path
"""
# check that file exists
if os.path.exists(path) is False:
yield False
else:
command = ['md5sum', path]
p = Popen(command, stdout = PIPE)
for line in p.communicate()[0].splitlines():
yield line.decode('... | [
"calc",
"MD5",
"based",
"on",
"path"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L18-L31 | [
"def",
"calcMD5",
"(",
"path",
")",
":",
"# check that file exists",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"path",
")",
"is",
"False",
":",
"yield",
"False",
"else",
":",
"command",
"=",
"[",
"'md5sum'",
",",
"path",
"]",
"p",
"=",
"Popen",
"(... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | md5check | * comfirm that downloaded files match md5 checksum on server
* if md5 is False, only check path for the download | ctbBio/ncbi_download.py | def md5check(f, ftp, md5, exclude):
"""
* comfirm that downloaded files match md5 checksum on server
* if md5 is False, only check path for the download
"""
files = glob(f)
# if no md5 file is specified: download files if path does not exist
if md5 is False:
if len(files) == 0:
... | def md5check(f, ftp, md5, exclude):
"""
* comfirm that downloaded files match md5 checksum on server
* if md5 is False, only check path for the download
"""
files = glob(f)
# if no md5 file is specified: download files if path does not exist
if md5 is False:
if len(files) == 0:
... | [
"*",
"comfirm",
"that",
"downloaded",
"files",
"match",
"md5",
"checksum",
"on",
"server",
"*",
"if",
"md5",
"is",
"False",
"only",
"check",
"path",
"for",
"the",
"download"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L33-L72 | [
"def",
"md5check",
"(",
"f",
",",
"ftp",
",",
"md5",
",",
"exclude",
")",
":",
"files",
"=",
"glob",
"(",
"f",
")",
"# if no md5 file is specified: download files if path does not exist",
"if",
"md5",
"is",
"False",
":",
"if",
"len",
"(",
"files",
")",
"==",... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | wget | download files with wget | ctbBio/ncbi_download.py | def wget(ftp, f = False, exclude = False, name = False, md5 = False, tries = 10):
"""
download files with wget
"""
# file name
if f is False:
f = ftp.rsplit('/', 1)[-1]
# downloaded file if it does not already exist
# check md5s on server (optional)
t = 0
while md5check(f, ft... | def wget(ftp, f = False, exclude = False, name = False, md5 = False, tries = 10):
"""
download files with wget
"""
# file name
if f is False:
f = ftp.rsplit('/', 1)[-1]
# downloaded file if it does not already exist
# check md5s on server (optional)
t = 0
while md5check(f, ft... | [
"download",
"files",
"with",
"wget"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L74-L97 | [
"def",
"wget",
"(",
"ftp",
",",
"f",
"=",
"False",
",",
"exclude",
"=",
"False",
",",
"name",
"=",
"False",
",",
"md5",
"=",
"False",
",",
"tries",
"=",
"10",
")",
":",
"# file name",
"if",
"f",
"is",
"False",
":",
"f",
"=",
"ftp",
".",
"rsplit... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | check | check that at least one of
queries is in list, l | ctbBio/ncbi_download.py | def check(line, queries):
"""
check that at least one of
queries is in list, l
"""
line = line.strip()
spLine = line.replace('.', ' ').split()
matches = set(spLine).intersection(queries)
if len(matches) > 0:
return matches, line.split('\t')
return matches, False | def check(line, queries):
"""
check that at least one of
queries is in list, l
"""
line = line.strip()
spLine = line.replace('.', ' ').split()
matches = set(spLine).intersection(queries)
if len(matches) > 0:
return matches, line.split('\t')
return matches, False | [
"check",
"that",
"at",
"least",
"one",
"of",
"queries",
"is",
"in",
"list",
"l"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L99-L109 | [
"def",
"check",
"(",
"line",
",",
"queries",
")",
":",
"line",
"=",
"line",
".",
"strip",
"(",
")",
"spLine",
"=",
"line",
".",
"replace",
"(",
"'.'",
",",
"' '",
")",
".",
"split",
"(",
")",
"matches",
"=",
"set",
"(",
"spLine",
")",
".",
"int... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | entrez | search entrez using specified database
and accession | ctbBio/ncbi_download.py | def entrez(db, acc):
"""
search entrez using specified database
and accession
"""
c1 = ['esearch', '-db', db, '-query', acc]
c2 = ['efetch', '-db', 'BioSample', '-format', 'docsum']
p1 = Popen(c1, stdout = PIPE, stderr = PIPE)
p2 = Popen(c2, stdin = p1.stdout, stdout = PIPE, stderr = PIP... | def entrez(db, acc):
"""
search entrez using specified database
and accession
"""
c1 = ['esearch', '-db', db, '-query', acc]
c2 = ['efetch', '-db', 'BioSample', '-format', 'docsum']
p1 = Popen(c1, stdout = PIPE, stderr = PIPE)
p2 = Popen(c2, stdin = p1.stdout, stdout = PIPE, stderr = PIP... | [
"search",
"entrez",
"using",
"specified",
"database",
"and",
"accession"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L111-L120 | [
"def",
"entrez",
"(",
"db",
",",
"acc",
")",
":",
"c1",
"=",
"[",
"'esearch'",
",",
"'-db'",
",",
"db",
",",
"'-query'",
",",
"acc",
"]",
"c2",
"=",
"[",
"'efetch'",
",",
"'-db'",
",",
"'BioSample'",
",",
"'-format'",
",",
"'docsum'",
"]",
"p1",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | searchAccession | attempt to use NCBI Entrez to get
BioSample ID | ctbBio/ncbi_download.py | def searchAccession(acc):
"""
attempt to use NCBI Entrez to get
BioSample ID
"""
# try genbank file
# genome database
out, error = entrez('genome', acc)
for line in out.splitlines():
line = line.decode('ascii').strip()
if 'Assembly_Accession' in line or 'BioSample' in lin... | def searchAccession(acc):
"""
attempt to use NCBI Entrez to get
BioSample ID
"""
# try genbank file
# genome database
out, error = entrez('genome', acc)
for line in out.splitlines():
line = line.decode('ascii').strip()
if 'Assembly_Accession' in line or 'BioSample' in lin... | [
"attempt",
"to",
"use",
"NCBI",
"Entrez",
"to",
"get",
"BioSample",
"ID"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L122-L156 | [
"def",
"searchAccession",
"(",
"acc",
")",
":",
"# try genbank file",
"# genome database",
"out",
",",
"error",
"=",
"entrez",
"(",
"'genome'",
",",
"acc",
")",
"for",
"line",
"in",
"out",
".",
"splitlines",
"(",
")",
":",
"line",
"=",
"line",
".",
"deco... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | getFTPs | download genome info from NCBI | ctbBio/ncbi_download.py | def getFTPs(accessions, ftp, search, exclude, convert = False, threads = 1, attempt = 1,
max_attempts = 2):
"""
download genome info from NCBI
"""
info = wget(ftp)[0]
allMatches = []
for genome in open(info, encoding = 'utf8'):
genome = str(genome)
matches, genomeInfo... | def getFTPs(accessions, ftp, search, exclude, convert = False, threads = 1, attempt = 1,
max_attempts = 2):
"""
download genome info from NCBI
"""
info = wget(ftp)[0]
allMatches = []
for genome in open(info, encoding = 'utf8'):
genome = str(genome)
matches, genomeInfo... | [
"download",
"genome",
"info",
"from",
"NCBI"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L158-L195 | [
"def",
"getFTPs",
"(",
"accessions",
",",
"ftp",
",",
"search",
",",
"exclude",
",",
"convert",
"=",
"False",
",",
"threads",
"=",
"1",
",",
"attempt",
"=",
"1",
",",
"max_attempts",
"=",
"2",
")",
":",
"info",
"=",
"wget",
"(",
"ftp",
")",
"[",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | download | download genomes from NCBI | ctbBio/ncbi_download.py | def download(args):
"""
download genomes from NCBI
"""
accessions, infoFTP = set(args['g']), args['i']
search, exclude = args['s'], args['e']
FTPs = getFTPs(accessions, infoFTP, search, exclude, threads = args['t'],
convert = args['convert'])
if args['test'] is True:
for ... | def download(args):
"""
download genomes from NCBI
"""
accessions, infoFTP = set(args['g']), args['i']
search, exclude = args['s'], args['e']
FTPs = getFTPs(accessions, infoFTP, search, exclude, threads = args['t'],
convert = args['convert'])
if args['test'] is True:
for ... | [
"download",
"genomes",
"from",
"NCBI"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/ncbi_download.py#L204-L221 | [
"def",
"download",
"(",
"args",
")",
":",
"accessions",
",",
"infoFTP",
"=",
"set",
"(",
"args",
"[",
"'g'",
"]",
")",
",",
"args",
"[",
"'i'",
"]",
"search",
",",
"exclude",
"=",
"args",
"[",
"'s'",
"]",
",",
"args",
"[",
"'e'",
"]",
"FTPs",
"... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | fix_fasta | remove pesky characters from fasta file header | ctbBio/fix_fasta.py | def fix_fasta(fasta):
"""
remove pesky characters from fasta file header
"""
for seq in parse_fasta(fasta):
seq[0] = remove_char(seq[0])
if len(seq[1]) > 0:
yield seq | def fix_fasta(fasta):
"""
remove pesky characters from fasta file header
"""
for seq in parse_fasta(fasta):
seq[0] = remove_char(seq[0])
if len(seq[1]) > 0:
yield seq | [
"remove",
"pesky",
"characters",
"from",
"fasta",
"file",
"header"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/fix_fasta.py#L18-L25 | [
"def",
"fix_fasta",
"(",
"fasta",
")",
":",
"for",
"seq",
"in",
"parse_fasta",
"(",
"fasta",
")",
":",
"seq",
"[",
"0",
"]",
"=",
"remove_char",
"(",
"seq",
"[",
"0",
"]",
")",
"if",
"len",
"(",
"seq",
"[",
"1",
"]",
")",
">",
"0",
":",
"yiel... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | plot_LDA | Plot transformed LDA data. | bin/LDA.py | def plot_LDA(X_lda, y_lda, class_colors, exp_var, style, fig_size, label_pad,
font_size, sids, dim=2, zangles=None, pt_size=250, out_fp=""):
"""
Plot transformed LDA data.
"""
cats = class_colors.keys()
fig = plt.figure(figsize=fig_size)
if dim == 3:
try:
assert ... | def plot_LDA(X_lda, y_lda, class_colors, exp_var, style, fig_size, label_pad,
font_size, sids, dim=2, zangles=None, pt_size=250, out_fp=""):
"""
Plot transformed LDA data.
"""
cats = class_colors.keys()
fig = plt.figure(figsize=fig_size)
if dim == 3:
try:
assert ... | [
"Plot",
"transformed",
"LDA",
"data",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/LDA.py#L45-L121 | [
"def",
"plot_LDA",
"(",
"X_lda",
",",
"y_lda",
",",
"class_colors",
",",
"exp_var",
",",
"style",
",",
"fig_size",
",",
"label_pad",
",",
"font_size",
",",
"sids",
",",
"dim",
"=",
"2",
",",
"zangles",
"=",
"None",
",",
"pt_size",
"=",
"250",
",",
"o... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | run_LDA | Run LinearDiscriminantAnalysis on input dataframe (df) and return
transformed data, scalings and explained variance by discriminants. | bin/LDA.py | def run_LDA(df):
"""
Run LinearDiscriminantAnalysis on input dataframe (df) and return
transformed data, scalings and explained variance by discriminants.
"""
# Prep variables for sklearn LDA
X = df.iloc[:, 1:df.shape[1]].values # input data matrix
y = df["Condition"].values ... | def run_LDA(df):
"""
Run LinearDiscriminantAnalysis on input dataframe (df) and return
transformed data, scalings and explained variance by discriminants.
"""
# Prep variables for sklearn LDA
X = df.iloc[:, 1:df.shape[1]].values # input data matrix
y = df["Condition"].values ... | [
"Run",
"LinearDiscriminantAnalysis",
"on",
"input",
"dataframe",
"(",
"df",
")",
"and",
"return",
"transformed",
"data",
"scalings",
"and",
"explained",
"variance",
"by",
"discriminants",
"."
] | smdabdoub/phylotoast | python | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/LDA.py#L124-L142 | [
"def",
"run_LDA",
"(",
"df",
")",
":",
"# Prep variables for sklearn LDA",
"X",
"=",
"df",
".",
"iloc",
"[",
":",
",",
"1",
":",
"df",
".",
"shape",
"[",
"1",
"]",
"]",
".",
"values",
"# input data matrix",
"y",
"=",
"df",
"[",
"\"Condition\"",
"]",
... | 0b74ef171e6a84761710548501dfac71285a58a3 |
train | _calc_frames | Compute a DataFrame summary of a Stats object. | pstatsviewer/viewer.py | def _calc_frames(stats):
"""
Compute a DataFrame summary of a Stats object.
"""
timings = []
callers = []
for key, values in iteritems(stats.stats):
timings.append(
pd.Series(
key + values[:-1],
index=timing_colnames,
)
)
... | def _calc_frames(stats):
"""
Compute a DataFrame summary of a Stats object.
"""
timings = []
callers = []
for key, values in iteritems(stats.stats):
timings.append(
pd.Series(
key + values[:-1],
index=timing_colnames,
)
)
... | [
"Compute",
"a",
"DataFrame",
"summary",
"of",
"a",
"Stats",
"object",
"."
] | ssanderson/pstats-view | python | https://github.com/ssanderson/pstats-view/blob/62148d4e01765806bc5e6bb40628cdb186482c05/pstatsviewer/viewer.py#L40-L66 | [
"def",
"_calc_frames",
"(",
"stats",
")",
":",
"timings",
"=",
"[",
"]",
"callers",
"=",
"[",
"]",
"for",
"key",
",",
"values",
"in",
"iteritems",
"(",
"stats",
".",
"stats",
")",
":",
"timings",
".",
"append",
"(",
"pd",
".",
"Series",
"(",
"key",... | 62148d4e01765806bc5e6bb40628cdb186482c05 |
train | unmapped | get unmapped reads | ctbBio/unmapped.py | def unmapped(sam, mates):
"""
get unmapped reads
"""
for read in sam:
if read.startswith('@') is True:
continue
read = read.strip().split()
if read[2] == '*' and read[6] == '*':
yield read
elif mates is True:
if read[2] == '*' or re... | def unmapped(sam, mates):
"""
get unmapped reads
"""
for read in sam:
if read.startswith('@') is True:
continue
read = read.strip().split()
if read[2] == '*' and read[6] == '*':
yield read
elif mates is True:
if read[2] == '*' or re... | [
"get",
"unmapped",
"reads"
] | christophertbrown/bioscripts | python | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/unmapped.py#L11-L26 | [
"def",
"unmapped",
"(",
"sam",
",",
"mates",
")",
":",
"for",
"read",
"in",
"sam",
":",
"if",
"read",
".",
"startswith",
"(",
"'@'",
")",
"is",
"True",
":",
"continue",
"read",
"=",
"read",
".",
"strip",
"(",
")",
".",
"split",
"(",
")",
"if",
... | 83b2566b3a5745437ec651cd6cafddd056846240 |
train | sugartex_preprocess | Preprocess text for SugarTeX Pandoc filter.
Replaces 'ˎ' with `$` (except `\ˎ`), replaces `\ˎ` with `ˎ` | sugartex/pre_sugartex.py | def sugartex_preprocess(source: str) -> str:
"""
Preprocess text for SugarTeX Pandoc filter.
Replaces 'ˎ' with `$` (except `\ˎ`), replaces `\ˎ` with `ˎ`
"""
rep = {r'\ˎ': 'ˎ', 'ˎ': '$'}
return re.sub(r'\\ˎ|ˎ', lambda m: rep[m.group(0)], source) | def sugartex_preprocess(source: str) -> str:
"""
Preprocess text for SugarTeX Pandoc filter.
Replaces 'ˎ' with `$` (except `\ˎ`), replaces `\ˎ` with `ˎ`
"""
rep = {r'\ˎ': 'ˎ', 'ˎ': '$'}
return re.sub(r'\\ˎ|ˎ', lambda m: rep[m.group(0)], source) | [
"Preprocess",
"text",
"for",
"SugarTeX",
"Pandoc",
"filter",
".",
"Replaces",
"ˎ",
"with",
"$",
"(",
"except",
"\\",
"ˎ",
")",
"replaces",
"\\",
"ˎ",
"with",
"ˎ"
] | kiwi0fruit/sugartex | python | https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/pre_sugartex.py#L13-L19 | [
"def",
"sugartex_preprocess",
"(",
"source",
":",
"str",
")",
"->",
"str",
":",
"rep",
"=",
"{",
"r'\\ˎ':",
" ",
"ˎ', ",
"'",
"': '",
"$",
"}",
"",
"return",
"re",
".",
"sub",
"(",
"r'\\\\ˎ|ˎ', ",
"l",
"mbda m",
" ",
"r",
"p[m",
".",
"g",
"r",
"o... | 9eb13703cb02d3e2163c9c5f29df280f6bf49cec |
train | sugartex_replace_all | Replace all with SugarTeX.
Runs ``sugartex_preprocess`` then iterates via regex and
replaces each math between '$...$'. | sugartex/pre_sugartex.py | def sugartex_replace_all(string):
"""
Replace all with SugarTeX.
Runs ``sugartex_preprocess`` then iterates via regex and
replaces each math between '$...$'.
"""
string = sugartex_preprocess(string).replace(r'\$', SESSION_ID)
return re.sub(
r'(?<=\$)[^$]*(?=\$)',
lambda m: su... | def sugartex_replace_all(string):
"""
Replace all with SugarTeX.
Runs ``sugartex_preprocess`` then iterates via regex and
replaces each math between '$...$'.
"""
string = sugartex_preprocess(string).replace(r'\$', SESSION_ID)
return re.sub(
r'(?<=\$)[^$]*(?=\$)',
lambda m: su... | [
"Replace",
"all",
"with",
"SugarTeX",
".",
"Runs",
"sugartex_preprocess",
"then",
"iterates",
"via",
"regex",
"and",
"replaces",
"each",
"math",
"between",
"$",
"...",
"$",
"."
] | kiwi0fruit/sugartex | python | https://github.com/kiwi0fruit/sugartex/blob/9eb13703cb02d3e2163c9c5f29df280f6bf49cec/sugartex/pre_sugartex.py#L25-L36 | [
"def",
"sugartex_replace_all",
"(",
"string",
")",
":",
"string",
"=",
"sugartex_preprocess",
"(",
"string",
")",
".",
"replace",
"(",
"r'\\$'",
",",
"SESSION_ID",
")",
"return",
"re",
".",
"sub",
"(",
"r'(?<=\\$)[^$]*(?=\\$)'",
",",
"lambda",
"m",
":",
"sug... | 9eb13703cb02d3e2163c9c5f29df280f6bf49cec |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.