repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 | partition stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|
sgaynetdinov/py-vkontakte | vk/auth.py | get_url_authcode_flow_user | def get_url_authcode_flow_user(client_id, redirect_uri, display="page", scope=None, state=None):
"""Authorization Code Flow for User Access Token
Use Authorization Code Flow to run VK API methods from the server side of an application.
Access token received this way is not bound to an ip address but set of... | python | def get_url_authcode_flow_user(client_id, redirect_uri, display="page", scope=None, state=None):
"""Authorization Code Flow for User Access Token
Use Authorization Code Flow to run VK API methods from the server side of an application.
Access token received this way is not bound to an ip address but set of... | [
"def",
"get_url_authcode_flow_user",
"(",
"client_id",
",",
"redirect_uri",
",",
"display",
"=",
"\"page\"",
",",
"scope",
"=",
"None",
",",
"state",
"=",
"None",
")",
":",
"url",
"=",
"\"https://oauth.vk.com/authorize\"",
"params",
"=",
"{",
"\"client_id\"",
":... | Authorization Code Flow for User Access Token
Use Authorization Code Flow to run VK API methods from the server side of an application.
Access token received this way is not bound to an ip address but set of permissions that can be granted is limited for security reasons.
Args:
client_id (int): Ap... | [
"Authorization",
"Code",
"Flow",
"for",
"User",
"Access",
"Token"
] | c09654f89008b5847418bb66f1f9c408cd7aa128 | https://github.com/sgaynetdinov/py-vkontakte/blob/c09654f89008b5847418bb66f1f9c408cd7aa128/vk/auth.py#L35-L76 | train |
Spinmob/spinmob | egg/example_from_wiki.py | get_fake_data | def get_fake_data(*a):
"""
Called whenever someone presses the "fire" button.
"""
# add columns of data to the databox
d['x'] = _n.linspace(0,10,100)
d['y'] = _n.cos(d['x']) + 0.1*_n.random.rand(100)
# update the curve
c.setData(d['x'], d['y']) | python | def get_fake_data(*a):
"""
Called whenever someone presses the "fire" button.
"""
# add columns of data to the databox
d['x'] = _n.linspace(0,10,100)
d['y'] = _n.cos(d['x']) + 0.1*_n.random.rand(100)
# update the curve
c.setData(d['x'], d['y']) | [
"def",
"get_fake_data",
"(",
"*",
"a",
")",
":",
"d",
"[",
"'x'",
"]",
"=",
"_n",
".",
"linspace",
"(",
"0",
",",
"10",
",",
"100",
")",
"d",
"[",
"'y'",
"]",
"=",
"_n",
".",
"cos",
"(",
"d",
"[",
"'x'",
"]",
")",
"+",
"0.1",
"*",
"_n",
... | Called whenever someone presses the "fire" button. | [
"Called",
"whenever",
"someone",
"presses",
"the",
"fire",
"button",
"."
] | f037f5df07f194bcd4a01f4d9916e57b9e8fb45a | https://github.com/Spinmob/spinmob/blob/f037f5df07f194bcd4a01f4d9916e57b9e8fb45a/egg/example_from_wiki.py#L49-L58 | train |
Spinmob/spinmob | egg/_temporary_fixes.py | SpinBox.selectNumber | def selectNumber(self):
"""
Select the numerical portion of the text to allow quick editing by the user.
"""
le = self.lineEdit()
text = asUnicode(le.text())
if self.opts['suffix'] == '':
le.setSelection(0, len(text))
else:
try:
... | python | def selectNumber(self):
"""
Select the numerical portion of the text to allow quick editing by the user.
"""
le = self.lineEdit()
text = asUnicode(le.text())
if self.opts['suffix'] == '':
le.setSelection(0, len(text))
else:
try:
... | [
"def",
"selectNumber",
"(",
"self",
")",
":",
"le",
"=",
"self",
".",
"lineEdit",
"(",
")",
"text",
"=",
"asUnicode",
"(",
"le",
".",
"text",
"(",
")",
")",
"if",
"self",
".",
"opts",
"[",
"'suffix'",
"]",
"==",
"''",
":",
"le",
".",
"setSelectio... | Select the numerical portion of the text to allow quick editing by the user. | [
"Select",
"the",
"numerical",
"portion",
"of",
"the",
"text",
"to",
"allow",
"quick",
"editing",
"by",
"the",
"user",
"."
] | f037f5df07f194bcd4a01f4d9916e57b9e8fb45a | https://github.com/Spinmob/spinmob/blob/f037f5df07f194bcd4a01f4d9916e57b9e8fb45a/egg/_temporary_fixes.py#L236-L249 | train |
Spinmob/spinmob | egg/_temporary_fixes.py | SpinBox.value | def value(self):
"""
Return the value of this SpinBox.
"""
if self.opts['int']:
return int(self.val)
else:
return float(self.val) | python | def value(self):
"""
Return the value of this SpinBox.
"""
if self.opts['int']:
return int(self.val)
else:
return float(self.val) | [
"def",
"value",
"(",
"self",
")",
":",
"if",
"self",
".",
"opts",
"[",
"'int'",
"]",
":",
"return",
"int",
"(",
"self",
".",
"val",
")",
"else",
":",
"return",
"float",
"(",
"self",
".",
"val",
")"
] | Return the value of this SpinBox. | [
"Return",
"the",
"value",
"of",
"this",
"SpinBox",
"."
] | f037f5df07f194bcd4a01f4d9916e57b9e8fb45a | https://github.com/Spinmob/spinmob/blob/f037f5df07f194bcd4a01f4d9916e57b9e8fb45a/egg/_temporary_fixes.py#L251-L259 | train |
Spinmob/spinmob | egg/_temporary_fixes.py | SpinBox.interpret | def interpret(self):
"""Return value of text. Return False if text is invalid, raise exception if text is intermediate"""
strn = self.lineEdit().text()
suf = self.opts['suffix']
if len(suf) > 0:
if strn[-len(suf):] != suf:
return False
#raise Excep... | python | def interpret(self):
"""Return value of text. Return False if text is invalid, raise exception if text is intermediate"""
strn = self.lineEdit().text()
suf = self.opts['suffix']
if len(suf) > 0:
if strn[-len(suf):] != suf:
return False
#raise Excep... | [
"def",
"interpret",
"(",
"self",
")",
":",
"strn",
"=",
"self",
".",
"lineEdit",
"(",
")",
".",
"text",
"(",
")",
"suf",
"=",
"self",
".",
"opts",
"[",
"'suffix'",
"]",
"if",
"len",
"(",
"suf",
")",
">",
"0",
":",
"if",
"strn",
"[",
"-",
"len... | Return value of text. Return False if text is invalid, raise exception if text is intermediate | [
"Return",
"value",
"of",
"text",
".",
"Return",
"False",
"if",
"text",
"is",
"invalid",
"raise",
"exception",
"if",
"text",
"is",
"intermediate"
] | f037f5df07f194bcd4a01f4d9916e57b9e8fb45a | https://github.com/Spinmob/spinmob/blob/f037f5df07f194bcd4a01f4d9916e57b9e8fb45a/egg/_temporary_fixes.py#L473-L489 | train |
Spinmob/spinmob | egg/_temporary_fixes.py | SpinBox.editingFinishedEvent | def editingFinishedEvent(self):
"""Edit has finished; set value."""
#print "Edit finished."
if asUnicode(self.lineEdit().text()) == self.lastText:
#print "no text change."
return
try:
val = self.interpret()
except:
return
... | python | def editingFinishedEvent(self):
"""Edit has finished; set value."""
#print "Edit finished."
if asUnicode(self.lineEdit().text()) == self.lastText:
#print "no text change."
return
try:
val = self.interpret()
except:
return
... | [
"def",
"editingFinishedEvent",
"(",
"self",
")",
":",
"if",
"asUnicode",
"(",
"self",
".",
"lineEdit",
"(",
")",
".",
"text",
"(",
")",
")",
"==",
"self",
".",
"lastText",
":",
"return",
"try",
":",
"val",
"=",
"self",
".",
"interpret",
"(",
")",
"... | Edit has finished; set value. | [
"Edit",
"has",
"finished",
";",
"set",
"value",
"."
] | f037f5df07f194bcd4a01f4d9916e57b9e8fb45a | https://github.com/Spinmob/spinmob/blob/f037f5df07f194bcd4a01f4d9916e57b9e8fb45a/egg/_temporary_fixes.py#L499-L516 | train |
sbaechler/django-scaffolding | scaffolding/management/commands/scaffold.py | Command.make_factory | def make_factory(self, cls, count):
""" Get the generators from the Scaffolding class within the model.
"""
field_names = cls._meta.get_all_field_names()
fields = {}
text = []
finalizer = None
scaffold = scaffolding.scaffold_for_model(cls)
for field_name ... | python | def make_factory(self, cls, count):
""" Get the generators from the Scaffolding class within the model.
"""
field_names = cls._meta.get_all_field_names()
fields = {}
text = []
finalizer = None
scaffold = scaffolding.scaffold_for_model(cls)
for field_name ... | [
"def",
"make_factory",
"(",
"self",
",",
"cls",
",",
"count",
")",
":",
"field_names",
"=",
"cls",
".",
"_meta",
".",
"get_all_field_names",
"(",
")",
"fields",
"=",
"{",
"}",
"text",
"=",
"[",
"]",
"finalizer",
"=",
"None",
"scaffold",
"=",
"scaffoldi... | Get the generators from the Scaffolding class within the model. | [
"Get",
"the",
"generators",
"from",
"the",
"Scaffolding",
"class",
"within",
"the",
"model",
"."
] | db78d99efe4fa1f3ef452fd0afd55fcdfdaea6db | https://github.com/sbaechler/django-scaffolding/blob/db78d99efe4fa1f3ef452fd0afd55fcdfdaea6db/scaffolding/management/commands/scaffold.py#L42-L66 | train |
KarchinLab/probabilistic2020 | prob2020/python/indel.py | compute_indel_length | def compute_indel_length(fs_df):
"""Computes the indel length accounting for wether it is an insertion or
deletion.
Parameters
----------
fs_df : pd.DataFrame
mutation input as dataframe only containing indel mutations
Returns
-------
indel_len : pd.Series
length of ind... | python | def compute_indel_length(fs_df):
"""Computes the indel length accounting for wether it is an insertion or
deletion.
Parameters
----------
fs_df : pd.DataFrame
mutation input as dataframe only containing indel mutations
Returns
-------
indel_len : pd.Series
length of ind... | [
"def",
"compute_indel_length",
"(",
"fs_df",
")",
":",
"indel_len",
"=",
"pd",
".",
"Series",
"(",
"index",
"=",
"fs_df",
".",
"index",
")",
"indel_len",
"[",
"fs_df",
"[",
"'Reference_Allele'",
"]",
"==",
"'-'",
"]",
"=",
"fs_df",
"[",
"'Tumor_Allele'",
... | Computes the indel length accounting for wether it is an insertion or
deletion.
Parameters
----------
fs_df : pd.DataFrame
mutation input as dataframe only containing indel mutations
Returns
-------
indel_len : pd.Series
length of indels | [
"Computes",
"the",
"indel",
"length",
"accounting",
"for",
"wether",
"it",
"is",
"an",
"insertion",
"or",
"deletion",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/indel.py#L125-L143 | train |
KarchinLab/probabilistic2020 | prob2020/python/indel.py | keep_indels | def keep_indels(mut_df,
indel_len_col=True,
indel_type_col=True):
"""Filters out all mutations that are not indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, resp... | python | def keep_indels(mut_df,
indel_len_col=True,
indel_type_col=True):
"""Filters out all mutations that are not indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, resp... | [
"def",
"keep_indels",
"(",
"mut_df",
",",
"indel_len_col",
"=",
"True",
",",
"indel_type_col",
"=",
"True",
")",
":",
"mut_df",
"=",
"mut_df",
"[",
"is_indel_annotation",
"(",
"mut_df",
")",
"]",
"if",
"indel_len_col",
":",
"mut_df",
".",
"loc",
"[",
":",
... | Filters out all mutations that are not indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, respectively.
Parameters
----------
mut_df : pd.DataFrame
mutation input file as a dataf... | [
"Filters",
"out",
"all",
"mutations",
"that",
"are",
"not",
"indels",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/indel.py#L146-L181 | train |
KarchinLab/probabilistic2020 | prob2020/python/indel.py | keep_frameshifts | def keep_frameshifts(mut_df,
indel_len_col=True):
"""Filters out all mutations that are not frameshift indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, respectively.
P... | python | def keep_frameshifts(mut_df,
indel_len_col=True):
"""Filters out all mutations that are not frameshift indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, respectively.
P... | [
"def",
"keep_frameshifts",
"(",
"mut_df",
",",
"indel_len_col",
"=",
"True",
")",
":",
"mut_df",
"=",
"mut_df",
"[",
"is_frameshift_annotation",
"(",
"mut_df",
")",
"]",
"if",
"indel_len_col",
":",
"mut_df",
".",
"loc",
"[",
":",
",",
"'indel len'",
"]",
"... | Filters out all mutations that are not frameshift indels.
Requires that one of the alleles have '-' indicating either an insertion
or deletion depending if found in reference allele or somatic allele
columns, respectively.
Parameters
----------
mut_df : pd.DataFrame
mutation input file... | [
"Filters",
"out",
"all",
"mutations",
"that",
"are",
"not",
"frameshift",
"indels",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/indel.py#L184-L210 | train |
KarchinLab/probabilistic2020 | prob2020/python/indel.py | is_frameshift_len | def is_frameshift_len(mut_df):
"""Simply returns a series indicating whether each corresponding mutation
is a frameshift.
This is based on the length of the indel. Thus may be fooled by frameshifts
at exon-intron boundaries or other odd cases.
Parameters
----------
mut_df : pd.DataFrame
... | python | def is_frameshift_len(mut_df):
"""Simply returns a series indicating whether each corresponding mutation
is a frameshift.
This is based on the length of the indel. Thus may be fooled by frameshifts
at exon-intron boundaries or other odd cases.
Parameters
----------
mut_df : pd.DataFrame
... | [
"def",
"is_frameshift_len",
"(",
"mut_df",
")",
":",
"if",
"'indel len'",
"in",
"mut_df",
".",
"columns",
":",
"indel_len",
"=",
"mut_df",
"[",
"'indel len'",
"]",
"else",
":",
"indel_len",
"=",
"compute_indel_length",
"(",
"mut_df",
")",
"is_fs",
"=",
"(",
... | Simply returns a series indicating whether each corresponding mutation
is a frameshift.
This is based on the length of the indel. Thus may be fooled by frameshifts
at exon-intron boundaries or other odd cases.
Parameters
----------
mut_df : pd.DataFrame
mutation input file as a datafra... | [
"Simply",
"returns",
"a",
"series",
"indicating",
"whether",
"each",
"corresponding",
"mutation",
"is",
"a",
"frameshift",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/indel.py#L213-L243 | train |
KarchinLab/probabilistic2020 | prob2020/python/indel.py | get_frameshift_lengths | def get_frameshift_lengths(num_bins):
"""Simple function that returns the lengths for each frameshift category
if `num_bins` number of frameshift categories are requested.
"""
fs_len = []
i = 1
tmp_bins = 0
while(tmp_bins<num_bins):
if i%3:
fs_len.append(i)
tm... | python | def get_frameshift_lengths(num_bins):
"""Simple function that returns the lengths for each frameshift category
if `num_bins` number of frameshift categories are requested.
"""
fs_len = []
i = 1
tmp_bins = 0
while(tmp_bins<num_bins):
if i%3:
fs_len.append(i)
tm... | [
"def",
"get_frameshift_lengths",
"(",
"num_bins",
")",
":",
"fs_len",
"=",
"[",
"]",
"i",
"=",
"1",
"tmp_bins",
"=",
"0",
"while",
"(",
"tmp_bins",
"<",
"num_bins",
")",
":",
"if",
"i",
"%",
"3",
":",
"fs_len",
".",
"append",
"(",
"i",
")",
"tmp_bi... | Simple function that returns the lengths for each frameshift category
if `num_bins` number of frameshift categories are requested. | [
"Simple",
"function",
"that",
"returns",
"the",
"lengths",
"for",
"each",
"frameshift",
"category",
"if",
"num_bins",
"number",
"of",
"frameshift",
"categories",
"are",
"requested",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/indel.py#L289-L301 | train |
KarchinLab/probabilistic2020 | prob2020/python/sequence_context.py | SequenceContext.random_context_pos | def random_context_pos(self, num, num_permutations, context):
"""Samples with replacement available positions matching the
sequence context.
Note: this method does random sampling only for an individual
sequence context.
Parameters
----------
num : int
... | python | def random_context_pos(self, num, num_permutations, context):
"""Samples with replacement available positions matching the
sequence context.
Note: this method does random sampling only for an individual
sequence context.
Parameters
----------
num : int
... | [
"def",
"random_context_pos",
"(",
"self",
",",
"num",
",",
"num_permutations",
",",
"context",
")",
":",
"if",
"not",
"self",
".",
"is_valid_context",
"(",
"context",
")",
":",
"error_msg",
"=",
"'Context ({0}) was never seen in sequence.'",
".",
"format",
"(",
... | Samples with replacement available positions matching the
sequence context.
Note: this method does random sampling only for an individual
sequence context.
Parameters
----------
num : int
Number of positions to sample for each permutation. This
i... | [
"Samples",
"with",
"replacement",
"available",
"positions",
"matching",
"the",
"sequence",
"context",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/sequence_context.py#L167-L205 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | retrieve_scores | def retrieve_scores(gname, sdir,
codon_pos, germ_aa, somatic_aa,
default_mga=5., default_vest=0,
no_file_flag=-1):
"""Retrieves scores from pickle files.
Used by summary script.
"""
# get variant types
#var_class = cutils.get_variant_clas... | python | def retrieve_scores(gname, sdir,
codon_pos, germ_aa, somatic_aa,
default_mga=5., default_vest=0,
no_file_flag=-1):
"""Retrieves scores from pickle files.
Used by summary script.
"""
# get variant types
#var_class = cutils.get_variant_clas... | [
"def",
"retrieve_scores",
"(",
"gname",
",",
"sdir",
",",
"codon_pos",
",",
"germ_aa",
",",
"somatic_aa",
",",
"default_mga",
"=",
"5.",
",",
"default_vest",
"=",
"0",
",",
"no_file_flag",
"=",
"-",
"1",
")",
":",
"mga_path",
"=",
"os",
".",
"path",
".... | Retrieves scores from pickle files.
Used by summary script. | [
"Retrieves",
"scores",
"from",
"pickle",
"files",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L15-L79 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | read_vest_pickle | def read_vest_pickle(gname, score_dir):
"""Read in VEST scores for given gene.
Parameters
----------
gname : str
name of gene
score_dir : str
directory containing vest scores
Returns
-------
gene_vest : dict or None
dict containing vest scores for gene. Returns ... | python | def read_vest_pickle(gname, score_dir):
"""Read in VEST scores for given gene.
Parameters
----------
gname : str
name of gene
score_dir : str
directory containing vest scores
Returns
-------
gene_vest : dict or None
dict containing vest scores for gene. Returns ... | [
"def",
"read_vest_pickle",
"(",
"gname",
",",
"score_dir",
")",
":",
"vest_path",
"=",
"os",
".",
"path",
".",
"join",
"(",
"score_dir",
",",
"gname",
"+",
"\".vest.pickle\"",
")",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"vest_path",
")",
":",
"if... | Read in VEST scores for given gene.
Parameters
----------
gname : str
name of gene
score_dir : str
directory containing vest scores
Returns
-------
gene_vest : dict or None
dict containing vest scores for gene. Returns None if not found. | [
"Read",
"in",
"VEST",
"scores",
"for",
"given",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L82-L107 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | compute_vest_stat | def compute_vest_stat(vest_dict, ref_aa, somatic_aa, codon_pos,
stat_func=np.mean,
default_val=0.0):
"""Compute missense VEST score statistic.
Note: non-missense mutations are intentially not filtered out and will take
a default value of zero.
Parameters
... | python | def compute_vest_stat(vest_dict, ref_aa, somatic_aa, codon_pos,
stat_func=np.mean,
default_val=0.0):
"""Compute missense VEST score statistic.
Note: non-missense mutations are intentially not filtered out and will take
a default value of zero.
Parameters
... | [
"def",
"compute_vest_stat",
"(",
"vest_dict",
",",
"ref_aa",
",",
"somatic_aa",
",",
"codon_pos",
",",
"stat_func",
"=",
"np",
".",
"mean",
",",
"default_val",
"=",
"0.0",
")",
":",
"if",
"vest_dict",
"is",
"None",
":",
"return",
"default_val",
"myscores",
... | Compute missense VEST score statistic.
Note: non-missense mutations are intentially not filtered out and will take
a default value of zero.
Parameters
----------
vest_dict : dict
dictionary containing vest scores across the gene of interest
ref_aa: list of str
list of reference... | [
"Compute",
"missense",
"VEST",
"score",
"statistic",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L110-L151 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | compute_mga_entropy_stat | def compute_mga_entropy_stat(mga_vec, codon_pos,
stat_func=np.mean,
default_val=0.0):
"""Compute MGA entropy conservation statistic
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for resi... | python | def compute_mga_entropy_stat(mga_vec, codon_pos,
stat_func=np.mean,
default_val=0.0):
"""Compute MGA entropy conservation statistic
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for resi... | [
"def",
"compute_mga_entropy_stat",
"(",
"mga_vec",
",",
"codon_pos",
",",
"stat_func",
"=",
"np",
".",
"mean",
",",
"default_val",
"=",
"0.0",
")",
":",
"if",
"mga_vec",
"is",
"None",
":",
"return",
"default_val",
"myscores",
"=",
"fetch_mga_scores",
"(",
"m... | Compute MGA entropy conservation statistic
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for residues
codon_pos : list of int
position of codon in protein sequence
stat_func : function, default=np.mean
function that calculat... | [
"Compute",
"MGA",
"entropy",
"conservation",
"statistic"
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L154-L188 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | fetch_vest_scores | def fetch_vest_scores(vest_dict,
ref_aa, somatic_aa, codon_pos,
default_vest=0.0):
"""Get VEST scores from pre-computed scores in dictionary.
Note: either all mutations should be missense or non-missense intended
to have value equal to default.
Parameters
... | python | def fetch_vest_scores(vest_dict,
ref_aa, somatic_aa, codon_pos,
default_vest=0.0):
"""Get VEST scores from pre-computed scores in dictionary.
Note: either all mutations should be missense or non-missense intended
to have value equal to default.
Parameters
... | [
"def",
"fetch_vest_scores",
"(",
"vest_dict",
",",
"ref_aa",
",",
"somatic_aa",
",",
"codon_pos",
",",
"default_vest",
"=",
"0.0",
")",
":",
"vest_score_list",
"=",
"[",
"]",
"for",
"i",
"in",
"range",
"(",
"len",
"(",
"somatic_aa",
")",
")",
":",
"if",
... | Get VEST scores from pre-computed scores in dictionary.
Note: either all mutations should be missense or non-missense intended
to have value equal to default.
Parameters
----------
vest_dict : dict
dictionary containing vest scores across the gene of interest
ref_aa: list of str
... | [
"Get",
"VEST",
"scores",
"from",
"pre",
"-",
"computed",
"scores",
"in",
"dictionary",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L191-L225 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | fetch_mga_scores | def fetch_mga_scores(mga_vec,
codon_pos,
default_mga=None):
"""Get MGAEntropy scores from pre-computed scores in array.
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for residues
codon_pos: list of ... | python | def fetch_mga_scores(mga_vec,
codon_pos,
default_mga=None):
"""Get MGAEntropy scores from pre-computed scores in array.
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for residues
codon_pos: list of ... | [
"def",
"fetch_mga_scores",
"(",
"mga_vec",
",",
"codon_pos",
",",
"default_mga",
"=",
"None",
")",
":",
"len_mga",
"=",
"len",
"(",
"mga_vec",
")",
"good_codon_pos",
"=",
"[",
"p",
"for",
"p",
"in",
"codon_pos",
"if",
"p",
"<",
"len_mga",
"]",
"if",
"g... | Get MGAEntropy scores from pre-computed scores in array.
Parameters
----------
mga_vec : np.array
numpy vector containing MGA Entropy conservation scores for residues
codon_pos: list of int
position of codon in protein sequence
default_mga: float or None, default=None
value ... | [
"Get",
"MGAEntropy",
"scores",
"from",
"pre",
"-",
"computed",
"scores",
"in",
"array",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L228-L258 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | read_neighbor_graph_pickle | def read_neighbor_graph_pickle(gname, graph_dir):
"""Read in neighbor graph for given gene.
Parameters
----------
gname : str
name of gene
graph_dir : str
directory containing gene graphs
Returns
-------
gene_graph : dict or None
neighbor graph as dict for gene.... | python | def read_neighbor_graph_pickle(gname, graph_dir):
"""Read in neighbor graph for given gene.
Parameters
----------
gname : str
name of gene
graph_dir : str
directory containing gene graphs
Returns
-------
gene_graph : dict or None
neighbor graph as dict for gene.... | [
"def",
"read_neighbor_graph_pickle",
"(",
"gname",
",",
"graph_dir",
")",
":",
"graph_path",
"=",
"os",
".",
"path",
".",
"join",
"(",
"graph_dir",
",",
"gname",
"+",
"\".pickle\"",
")",
"if",
"os",
".",
"path",
".",
"exists",
"(",
"graph_path",
")",
":"... | Read in neighbor graph for given gene.
Parameters
----------
gname : str
name of gene
graph_dir : str
directory containing gene graphs
Returns
-------
gene_graph : dict or None
neighbor graph as dict for gene. Returns None if not found. | [
"Read",
"in",
"neighbor",
"graph",
"for",
"given",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L261-L282 | train |
KarchinLab/probabilistic2020 | prob2020/python/scores.py | compute_ng_stat | def compute_ng_stat(gene_graph, pos_ct, alpha=.5):
"""Compute the clustering score for the gene on its neighbor graph.
Parameters
----------
gene_graph : dict
Graph of spatially near codons. keys = nodes, edges = key -> value.
pos_ct : dict
missense mutation count for each codon
... | python | def compute_ng_stat(gene_graph, pos_ct, alpha=.5):
"""Compute the clustering score for the gene on its neighbor graph.
Parameters
----------
gene_graph : dict
Graph of spatially near codons. keys = nodes, edges = key -> value.
pos_ct : dict
missense mutation count for each codon
... | [
"def",
"compute_ng_stat",
"(",
"gene_graph",
",",
"pos_ct",
",",
"alpha",
"=",
".5",
")",
":",
"if",
"not",
"len",
"(",
"pos_ct",
")",
":",
"return",
"1.0",
",",
"0",
"max_pos",
"=",
"max",
"(",
"gene_graph",
")",
"codon_vals",
"=",
"np",
".",
"zeros... | Compute the clustering score for the gene on its neighbor graph.
Parameters
----------
gene_graph : dict
Graph of spatially near codons. keys = nodes, edges = key -> value.
pos_ct : dict
missense mutation count for each codon
alpha : float
smoothing factor
Returns
-... | [
"Compute",
"the",
"clustering",
"score",
"for",
"the",
"gene",
"on",
"its",
"neighbor",
"graph",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/scores.py#L285-L334 | train |
KarchinLab/probabilistic2020 | prob2020/python/count_frameshifts.py | count_frameshift_total | def count_frameshift_total(mut_df,
bed_path,
use_unmapped=False,
to_zero_based=False):
"""Count frameshifts for each gene.
Parameters
----------
mut_df : pd.DataFrame
mutation input
bed_path : str
path ... | python | def count_frameshift_total(mut_df,
bed_path,
use_unmapped=False,
to_zero_based=False):
"""Count frameshifts for each gene.
Parameters
----------
mut_df : pd.DataFrame
mutation input
bed_path : str
path ... | [
"def",
"count_frameshift_total",
"(",
"mut_df",
",",
"bed_path",
",",
"use_unmapped",
"=",
"False",
",",
"to_zero_based",
"=",
"False",
")",
":",
"if",
"to_zero_based",
":",
"mut_df",
"[",
"'Start_Position'",
"]",
"=",
"mut_df",
"[",
"'Start_Position'",
"]",
"... | Count frameshifts for each gene.
Parameters
----------
mut_df : pd.DataFrame
mutation input
bed_path : str
path to BED file containing reference tx for genes
use_unmapped : Bool
flag indicating whether to include frameshifts not mapping
to reference tx
to_zero_ba... | [
"Count",
"frameshifts",
"for",
"each",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/count_frameshifts.py#L6-L64 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | _fetch_3ss_fasta | def _fetch_3ss_fasta(fasta, gene_name, exon_num,
chrom, strand, start, end):
"""Retreives the 3' SS sequence flanking the specified exon.
Returns a string in fasta format with the first line containing
a ">" and the second line contains the two base pairs of 3' SS.
Parameters
... | python | def _fetch_3ss_fasta(fasta, gene_name, exon_num,
chrom, strand, start, end):
"""Retreives the 3' SS sequence flanking the specified exon.
Returns a string in fasta format with the first line containing
a ">" and the second line contains the two base pairs of 3' SS.
Parameters
... | [
"def",
"_fetch_3ss_fasta",
"(",
"fasta",
",",
"gene_name",
",",
"exon_num",
",",
"chrom",
",",
"strand",
",",
"start",
",",
"end",
")",
":",
"if",
"strand",
"==",
"'-'",
":",
"ss_seq",
"=",
"fasta",
".",
"fetch",
"(",
"reference",
"=",
"chrom",
",",
... | Retreives the 3' SS sequence flanking the specified exon.
Returns a string in fasta format with the first line containing
a ">" and the second line contains the two base pairs of 3' SS.
Parameters
----------
fasta : pysam.Fastafile
fasta object from pysam
gene_name : str
gene n... | [
"Retreives",
"the",
"3",
"SS",
"sequence",
"flanking",
"the",
"specified",
"exon",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L153-L195 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | fetch_gene_fasta | def fetch_gene_fasta(gene_bed, fasta_obj):
"""Retreive gene sequences in FASTA format.
Parameters
----------
gene_bed : BedLine
BedLine object representing a single gene
fasta_obj : pysam.Fastafile
fasta object for index retreival of sequence
Returns
-------
gene_fasta ... | python | def fetch_gene_fasta(gene_bed, fasta_obj):
"""Retreive gene sequences in FASTA format.
Parameters
----------
gene_bed : BedLine
BedLine object representing a single gene
fasta_obj : pysam.Fastafile
fasta object for index retreival of sequence
Returns
-------
gene_fasta ... | [
"def",
"fetch_gene_fasta",
"(",
"gene_bed",
",",
"fasta_obj",
")",
":",
"gene_fasta",
"=",
"''",
"strand",
"=",
"gene_bed",
".",
"strand",
"exons",
"=",
"gene_bed",
".",
"get_exons",
"(",
")",
"if",
"strand",
"==",
"'-'",
":",
"exons",
".",
"reverse",
"(... | Retreive gene sequences in FASTA format.
Parameters
----------
gene_bed : BedLine
BedLine object representing a single gene
fasta_obj : pysam.Fastafile
fasta object for index retreival of sequence
Returns
-------
gene_fasta : str
sequence of gene in FASTA format | [
"Retreive",
"gene",
"sequences",
"in",
"FASTA",
"format",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L198-L251 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | GeneSequence._reset_seq | def _reset_seq(self):
"""Updates attributes for gene represented in the self.bed attribute.
Sequences are always upper case.
"""
exon_seq_list, five_ss_seq_list, three_ss_seq_list = self._fetch_seq()
self.exon_seq = ''.join(exon_seq_list)
self.three_prime_seq = three_ss_... | python | def _reset_seq(self):
"""Updates attributes for gene represented in the self.bed attribute.
Sequences are always upper case.
"""
exon_seq_list, five_ss_seq_list, three_ss_seq_list = self._fetch_seq()
self.exon_seq = ''.join(exon_seq_list)
self.three_prime_seq = three_ss_... | [
"def",
"_reset_seq",
"(",
"self",
")",
":",
"exon_seq_list",
",",
"five_ss_seq_list",
",",
"three_ss_seq_list",
"=",
"self",
".",
"_fetch_seq",
"(",
")",
"self",
".",
"exon_seq",
"=",
"''",
".",
"join",
"(",
"exon_seq_list",
")",
"self",
".",
"three_prime_se... | Updates attributes for gene represented in the self.bed attribute.
Sequences are always upper case. | [
"Updates",
"attributes",
"for",
"gene",
"represented",
"in",
"the",
"self",
".",
"bed",
"attribute",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L23-L32 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | GeneSequence.add_germline_variants | def add_germline_variants(self, germline_nucs, coding_pos):
"""Add potential germline variants into the nucleotide sequence.
Sequenced individuals may potentially have a SNP at a somatic mutation position.
Therefore they may differ from the reference genome. This method updates the gene
... | python | def add_germline_variants(self, germline_nucs, coding_pos):
"""Add potential germline variants into the nucleotide sequence.
Sequenced individuals may potentially have a SNP at a somatic mutation position.
Therefore they may differ from the reference genome. This method updates the gene
... | [
"def",
"add_germline_variants",
"(",
"self",
",",
"germline_nucs",
",",
"coding_pos",
")",
":",
"if",
"len",
"(",
"germline_nucs",
")",
"!=",
"len",
"(",
"coding_pos",
")",
":",
"raise",
"ValueError",
"(",
"'Each germline nucleotide should have a coding position'",
... | Add potential germline variants into the nucleotide sequence.
Sequenced individuals may potentially have a SNP at a somatic mutation position.
Therefore they may differ from the reference genome. This method updates the gene
germline gene sequence to match the actual individual.
Parame... | [
"Add",
"potential",
"germline",
"variants",
"into",
"the",
"nucleotide",
"sequence",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L34-L60 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | GeneSequence._to_upper | def _to_upper(self):
"""Convert sequences to upper case."""
self.exon_seq = self.exon_seq.upper()
self.three_prime_seq = [s.upper() for s in self.three_prime_seq]
self.five_prime_seq = [s.upper() for s in self.five_prime_seq] | python | def _to_upper(self):
"""Convert sequences to upper case."""
self.exon_seq = self.exon_seq.upper()
self.three_prime_seq = [s.upper() for s in self.three_prime_seq]
self.five_prime_seq = [s.upper() for s in self.five_prime_seq] | [
"def",
"_to_upper",
"(",
"self",
")",
":",
"self",
".",
"exon_seq",
"=",
"self",
".",
"exon_seq",
".",
"upper",
"(",
")",
"self",
".",
"three_prime_seq",
"=",
"[",
"s",
".",
"upper",
"(",
")",
"for",
"s",
"in",
"self",
".",
"three_prime_seq",
"]",
... | Convert sequences to upper case. | [
"Convert",
"sequences",
"to",
"upper",
"case",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L62-L66 | train |
KarchinLab/probabilistic2020 | prob2020/python/gene_sequence.py | GeneSequence._fetch_seq | def _fetch_seq(self):
"""Fetches gene sequence from PySAM fasta object.
Returns
-------
exons : list of str
list of exon nucleotide sequences
five_prime_ss : list of str
list of 5' splice site sequences
three_prime_ss : list of str
lis... | python | def _fetch_seq(self):
"""Fetches gene sequence from PySAM fasta object.
Returns
-------
exons : list of str
list of exon nucleotide sequences
five_prime_ss : list of str
list of 5' splice site sequences
three_prime_ss : list of str
lis... | [
"def",
"_fetch_seq",
"(",
"self",
")",
":",
"exons",
"=",
"[",
"]",
"three_prime_ss",
"=",
"[",
"]",
"five_prime_ss",
"=",
"[",
"]",
"num_exons",
"=",
"self",
".",
"bed",
".",
"get_num_exons",
"(",
")",
"for",
"i",
"in",
"range",
"(",
"num_exons",
")... | Fetches gene sequence from PySAM fasta object.
Returns
-------
exons : list of str
list of exon nucleotide sequences
five_prime_ss : list of str
list of 5' splice site sequences
three_prime_ss : list of str
list of 3' splice site sequences | [
"Fetches",
"gene",
"sequence",
"from",
"PySAM",
"fasta",
"object",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/gene_sequence.py#L68-L106 | train |
KarchinLab/probabilistic2020 | scripts/check_mutations.py | correct_chrom_names | def correct_chrom_names(chroms):
"""Make sure chromosome names follow UCSC chr convention."""
chrom_list = []
for chrom in chroms:
# fix chrom numbering
chrom = str(chrom)
chrom = chrom.replace('23', 'X')
chrom = chrom.replace('24', 'Y')
chrom = chrom.replace('25', 'M... | python | def correct_chrom_names(chroms):
"""Make sure chromosome names follow UCSC chr convention."""
chrom_list = []
for chrom in chroms:
# fix chrom numbering
chrom = str(chrom)
chrom = chrom.replace('23', 'X')
chrom = chrom.replace('24', 'Y')
chrom = chrom.replace('25', 'M... | [
"def",
"correct_chrom_names",
"(",
"chroms",
")",
":",
"chrom_list",
"=",
"[",
"]",
"for",
"chrom",
"in",
"chroms",
":",
"chrom",
"=",
"str",
"(",
"chrom",
")",
"chrom",
"=",
"chrom",
".",
"replace",
"(",
"'23'",
",",
"'X'",
")",
"chrom",
"=",
"chrom... | Make sure chromosome names follow UCSC chr convention. | [
"Make",
"sure",
"chromosome",
"names",
"follow",
"UCSC",
"chr",
"convention",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/scripts/check_mutations.py#L23-L35 | train |
KarchinLab/probabilistic2020 | prob2020/python/p_value.py | fishers_method | def fishers_method(pvals):
"""Fisher's method for combining independent p-values."""
pvals = np.asarray(pvals)
degrees_of_freedom = 2 * pvals.size
chisq_stat = np.sum(-2*np.log(pvals))
fishers_pval = stats.chi2.sf(chisq_stat, degrees_of_freedom)
return fishers_pval | python | def fishers_method(pvals):
"""Fisher's method for combining independent p-values."""
pvals = np.asarray(pvals)
degrees_of_freedom = 2 * pvals.size
chisq_stat = np.sum(-2*np.log(pvals))
fishers_pval = stats.chi2.sf(chisq_stat, degrees_of_freedom)
return fishers_pval | [
"def",
"fishers_method",
"(",
"pvals",
")",
":",
"pvals",
"=",
"np",
".",
"asarray",
"(",
"pvals",
")",
"degrees_of_freedom",
"=",
"2",
"*",
"pvals",
".",
"size",
"chisq_stat",
"=",
"np",
".",
"sum",
"(",
"-",
"2",
"*",
"np",
".",
"log",
"(",
"pval... | Fisher's method for combining independent p-values. | [
"Fisher",
"s",
"method",
"for",
"combining",
"independent",
"p",
"-",
"values",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/p_value.py#L18-L24 | train |
KarchinLab/probabilistic2020 | prob2020/python/p_value.py | cummin | def cummin(x):
"""A python implementation of the cummin function in R"""
for i in range(1, len(x)):
if x[i-1] < x[i]:
x[i] = x[i-1]
return x | python | def cummin(x):
"""A python implementation of the cummin function in R"""
for i in range(1, len(x)):
if x[i-1] < x[i]:
x[i] = x[i-1]
return x | [
"def",
"cummin",
"(",
"x",
")",
":",
"for",
"i",
"in",
"range",
"(",
"1",
",",
"len",
"(",
"x",
")",
")",
":",
"if",
"x",
"[",
"i",
"-",
"1",
"]",
"<",
"x",
"[",
"i",
"]",
":",
"x",
"[",
"i",
"]",
"=",
"x",
"[",
"i",
"-",
"1",
"]",
... | A python implementation of the cummin function in R | [
"A",
"python",
"implementation",
"of",
"the",
"cummin",
"function",
"in",
"R"
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/p_value.py#L27-L32 | train |
KarchinLab/probabilistic2020 | prob2020/python/p_value.py | bh_fdr | def bh_fdr(pval):
"""A python implementation of the Benjamani-Hochberg FDR method.
This code should always give precisely the same answer as using
p.adjust(pval, method="BH") in R.
Parameters
----------
pval : list or array
list/array of p-values
Returns
-------
pval_adj :... | python | def bh_fdr(pval):
"""A python implementation of the Benjamani-Hochberg FDR method.
This code should always give precisely the same answer as using
p.adjust(pval, method="BH") in R.
Parameters
----------
pval : list or array
list/array of p-values
Returns
-------
pval_adj :... | [
"def",
"bh_fdr",
"(",
"pval",
")",
":",
"pval_array",
"=",
"np",
".",
"array",
"(",
"pval",
")",
"sorted_order",
"=",
"np",
".",
"argsort",
"(",
"pval_array",
")",
"original_order",
"=",
"np",
".",
"argsort",
"(",
"sorted_order",
")",
"pval_array",
"=",
... | A python implementation of the Benjamani-Hochberg FDR method.
This code should always give precisely the same answer as using
p.adjust(pval, method="BH") in R.
Parameters
----------
pval : list or array
list/array of p-values
Returns
-------
pval_adj : np.array
adjuste... | [
"A",
"python",
"implementation",
"of",
"the",
"Benjamani",
"-",
"Hochberg",
"FDR",
"method",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/p_value.py#L35-L61 | train |
KarchinLab/probabilistic2020 | prob2020/python/p_value.py | calc_deleterious_p_value | def calc_deleterious_p_value(mut_info,
unmapped_mut_info,
sc,
gs,
bed,
num_permutations,
stop_thresh,
del_threshold,
... | python | def calc_deleterious_p_value(mut_info,
unmapped_mut_info,
sc,
gs,
bed,
num_permutations,
stop_thresh,
del_threshold,
... | [
"def",
"calc_deleterious_p_value",
"(",
"mut_info",
",",
"unmapped_mut_info",
",",
"sc",
",",
"gs",
",",
"bed",
",",
"num_permutations",
",",
"stop_thresh",
",",
"del_threshold",
",",
"pseudo_count",
",",
"seed",
"=",
"None",
")",
":",
"if",
"len",
"(",
"mut... | Calculates the p-value for the number of inactivating SNV mutations.
Calculates p-value based on how many simulations exceed the observed value.
Parameters
----------
mut_info : dict
contains codon and amino acid residue information for mutations mappable
to provided reference tx.
... | [
"Calculates",
"the",
"p",
"-",
"value",
"for",
"the",
"number",
"of",
"inactivating",
"SNV",
"mutations",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/p_value.py#L64-L145 | train |
KarchinLab/probabilistic2020 | prob2020/python/p_value.py | calc_protein_p_value | def calc_protein_p_value(mut_info,
unmapped_mut_info,
sc,
gs,
bed,
graph_dir,
num_permutations,
stop_thresh,
min_recurre... | python | def calc_protein_p_value(mut_info,
unmapped_mut_info,
sc,
gs,
bed,
graph_dir,
num_permutations,
stop_thresh,
min_recurre... | [
"def",
"calc_protein_p_value",
"(",
"mut_info",
",",
"unmapped_mut_info",
",",
"sc",
",",
"gs",
",",
"bed",
",",
"graph_dir",
",",
"num_permutations",
",",
"stop_thresh",
",",
"min_recurrent",
",",
"min_fraction",
")",
":",
"if",
"len",
"(",
"mut_info",
")",
... | Computes the p-value for clustering on a neighbor graph composed
of codons connected with edges if they are spatially near in 3D protein
structure.
Parameters
----------
Returns
------- | [
"Computes",
"the",
"p",
"-",
"value",
"for",
"clustering",
"on",
"a",
"neighbor",
"graph",
"composed",
"of",
"codons",
"connected",
"with",
"edges",
"if",
"they",
"are",
"spatially",
"near",
"in",
"3D",
"protein",
"structure",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/p_value.py#L291-L369 | train |
KarchinLab/probabilistic2020 | prob2020/python/mymath.py | shannon_entropy | def shannon_entropy(p):
"""Calculates shannon entropy in bits.
Parameters
----------
p : np.array
array of probabilities
Returns
-------
shannon entropy in bits
"""
return -np.sum(np.where(p!=0, p * np.log2(p), 0)) | python | def shannon_entropy(p):
"""Calculates shannon entropy in bits.
Parameters
----------
p : np.array
array of probabilities
Returns
-------
shannon entropy in bits
"""
return -np.sum(np.where(p!=0, p * np.log2(p), 0)) | [
"def",
"shannon_entropy",
"(",
"p",
")",
":",
"return",
"-",
"np",
".",
"sum",
"(",
"np",
".",
"where",
"(",
"p",
"!=",
"0",
",",
"p",
"*",
"np",
".",
"log2",
"(",
"p",
")",
",",
"0",
")",
")"
] | Calculates shannon entropy in bits.
Parameters
----------
p : np.array
array of probabilities
Returns
-------
shannon entropy in bits | [
"Calculates",
"shannon",
"entropy",
"in",
"bits",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mymath.py#L7-L19 | train |
KarchinLab/probabilistic2020 | prob2020/python/mymath.py | js_divergence | def js_divergence(p, q):
"""Compute the Jensen-Shannon Divergence between two discrete distributions.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : np.array
probability mass array (sums to 1)
Returns
-------
js_div : float
js divergen... | python | def js_divergence(p, q):
"""Compute the Jensen-Shannon Divergence between two discrete distributions.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : np.array
probability mass array (sums to 1)
Returns
-------
js_div : float
js divergen... | [
"def",
"js_divergence",
"(",
"p",
",",
"q",
")",
":",
"m",
"=",
".5",
"*",
"(",
"p",
"+",
"q",
")",
"js_div",
"=",
".5",
"*",
"kl_divergence",
"(",
"p",
",",
"m",
")",
"+",
".5",
"*",
"kl_divergence",
"(",
"q",
",",
"m",
")",
"return",
"js_di... | Compute the Jensen-Shannon Divergence between two discrete distributions.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : np.array
probability mass array (sums to 1)
Returns
-------
js_div : float
js divergence between the two distrubtions | [
"Compute",
"the",
"Jensen",
"-",
"Shannon",
"Divergence",
"between",
"two",
"discrete",
"distributions",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mymath.py#L112-L129 | train |
KarchinLab/probabilistic2020 | prob2020/python/mymath.py | js_distance | def js_distance(p, q):
"""Compute the Jensen-Shannon distance between two discrete distributions.
NOTE: JS divergence is not a metric but the sqrt of JS divergence is a
metric and is called the JS distance.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : n... | python | def js_distance(p, q):
"""Compute the Jensen-Shannon distance between two discrete distributions.
NOTE: JS divergence is not a metric but the sqrt of JS divergence is a
metric and is called the JS distance.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : n... | [
"def",
"js_distance",
"(",
"p",
",",
"q",
")",
":",
"js_dist",
"=",
"np",
".",
"sqrt",
"(",
"js_divergence",
"(",
"p",
",",
"q",
")",
")",
"return",
"js_dist"
] | Compute the Jensen-Shannon distance between two discrete distributions.
NOTE: JS divergence is not a metric but the sqrt of JS divergence is a
metric and is called the JS distance.
Parameters
----------
p : np.array
probability mass array (sums to 1)
q : np.array
probability ma... | [
"Compute",
"the",
"Jensen",
"-",
"Shannon",
"distance",
"between",
"two",
"discrete",
"distributions",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mymath.py#L132-L151 | train |
KarchinLab/probabilistic2020 | prob2020/python/bed_line.py | BedLine._init_exons | def _init_exons(self):
"""Sets a list of position intervals for each exon.
Only coding regions as defined by thickStart and thickEnd are kept.
Exons are stored in the self.exons attribute.
"""
exon_starts = [self.chrom_start + int(s)
for s in self.bed_tupl... | python | def _init_exons(self):
"""Sets a list of position intervals for each exon.
Only coding regions as defined by thickStart and thickEnd are kept.
Exons are stored in the self.exons attribute.
"""
exon_starts = [self.chrom_start + int(s)
for s in self.bed_tupl... | [
"def",
"_init_exons",
"(",
"self",
")",
":",
"exon_starts",
"=",
"[",
"self",
".",
"chrom_start",
"+",
"int",
"(",
"s",
")",
"for",
"s",
"in",
"self",
".",
"bed_tuple",
".",
"blockStarts",
".",
"strip",
"(",
"','",
")",
".",
"split",
"(",
"','",
")... | Sets a list of position intervals for each exon.
Only coding regions as defined by thickStart and thickEnd are kept.
Exons are stored in the self.exons attribute. | [
"Sets",
"a",
"list",
"of",
"position",
"intervals",
"for",
"each",
"exon",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/bed_line.py#L109-L129 | train |
KarchinLab/probabilistic2020 | prob2020/python/bed_line.py | BedLine.init_genome_coordinates | def init_genome_coordinates(self) :
"""Creates the self.seqpos2genome dictionary that converts positions
relative to the sequence to genome coordinates."""
self.seqpos2genome = {}
# record genome positions for each sequence position
seq_pos = 0
for estart, eend in self.e... | python | def init_genome_coordinates(self) :
"""Creates the self.seqpos2genome dictionary that converts positions
relative to the sequence to genome coordinates."""
self.seqpos2genome = {}
# record genome positions for each sequence position
seq_pos = 0
for estart, eend in self.e... | [
"def",
"init_genome_coordinates",
"(",
"self",
")",
":",
"self",
".",
"seqpos2genome",
"=",
"{",
"}",
"seq_pos",
"=",
"0",
"for",
"estart",
",",
"eend",
"in",
"self",
".",
"exons",
":",
"for",
"genome_pos",
"in",
"range",
"(",
"estart",
",",
"eend",
")... | Creates the self.seqpos2genome dictionary that converts positions
relative to the sequence to genome coordinates. | [
"Creates",
"the",
"self",
".",
"seqpos2genome",
"dictionary",
"that",
"converts",
"positions",
"relative",
"to",
"the",
"sequence",
"to",
"genome",
"coordinates",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/bed_line.py#L157-L197 | train |
KarchinLab/probabilistic2020 | prob2020/python/bed_line.py | BedLine.query_position | def query_position(self, strand, chr, genome_coord):
"""Provides the relative position on the coding sequence for a given
genomic position.
Parameters
----------
chr : str
chromosome, provided to check validity of query
genome_coord : int
0-based ... | python | def query_position(self, strand, chr, genome_coord):
"""Provides the relative position on the coding sequence for a given
genomic position.
Parameters
----------
chr : str
chromosome, provided to check validity of query
genome_coord : int
0-based ... | [
"def",
"query_position",
"(",
"self",
",",
"strand",
",",
"chr",
",",
"genome_coord",
")",
":",
"pos",
"=",
"None",
"if",
"chr",
"!=",
"self",
".",
"chrom",
":",
"pass",
"if",
"type",
"(",
"genome_coord",
")",
"is",
"list",
":",
"pos_left",
"=",
"sel... | Provides the relative position on the coding sequence for a given
genomic position.
Parameters
----------
chr : str
chromosome, provided to check validity of query
genome_coord : int
0-based position for mutation, actually used to get relative coding pos
... | [
"Provides",
"the",
"relative",
"position",
"on",
"the",
"coding",
"sequence",
"for",
"a",
"given",
"genomic",
"position",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/bed_line.py#L199-L260 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | start_logging | def start_logging(log_file='', log_level='INFO', verbose=False):
"""Start logging information into the log directory.
If os.devnull is specified as the log_file then the log file will
not actually be written to a file.
"""
if not log_file:
# create log directory if it doesn't exist
... | python | def start_logging(log_file='', log_level='INFO', verbose=False):
"""Start logging information into the log directory.
If os.devnull is specified as the log_file then the log file will
not actually be written to a file.
"""
if not log_file:
# create log directory if it doesn't exist
... | [
"def",
"start_logging",
"(",
"log_file",
"=",
"''",
",",
"log_level",
"=",
"'INFO'",
",",
"verbose",
"=",
"False",
")",
":",
"if",
"not",
"log_file",
":",
"log_dir",
"=",
"os",
".",
"path",
".",
"abspath",
"(",
"'log'",
")",
"+",
"'/'",
"if",
"not",
... | Start logging information into the log directory.
If os.devnull is specified as the log_file then the log file will
not actually be written to a file. | [
"Start",
"logging",
"information",
"into",
"the",
"log",
"directory",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L75-L119 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | log_error_decorator | def log_error_decorator(f):
"""Writes exception to log file if occured in decorated function.
This decorator wrapper is needed for multiprocess logging since otherwise
the python multiprocessing module will obscure the actual line of the error.
"""
@wraps(f)
def wrapper(*args, **kwds):
... | python | def log_error_decorator(f):
"""Writes exception to log file if occured in decorated function.
This decorator wrapper is needed for multiprocess logging since otherwise
the python multiprocessing module will obscure the actual line of the error.
"""
@wraps(f)
def wrapper(*args, **kwds):
... | [
"def",
"log_error_decorator",
"(",
"f",
")",
":",
"@",
"wraps",
"(",
"f",
")",
"def",
"wrapper",
"(",
"*",
"args",
",",
"**",
"kwds",
")",
":",
"try",
":",
"result",
"=",
"f",
"(",
"*",
"args",
",",
"**",
"kwds",
")",
"return",
"result",
"except"... | Writes exception to log file if occured in decorated function.
This decorator wrapper is needed for multiprocess logging since otherwise
the python multiprocessing module will obscure the actual line of the error. | [
"Writes",
"exception",
"to",
"log",
"file",
"if",
"occured",
"in",
"decorated",
"function",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L122-L138 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | filter_list | def filter_list(mylist, bad_ixs):
"""Removes indices from a list.
All elements in bad_ixs will be removed from the list.
Parameters
----------
mylist : list
list to filter out specific indices
bad_ixs : list of ints
indices to remove from list
Returns
-------
mylis... | python | def filter_list(mylist, bad_ixs):
"""Removes indices from a list.
All elements in bad_ixs will be removed from the list.
Parameters
----------
mylist : list
list to filter out specific indices
bad_ixs : list of ints
indices to remove from list
Returns
-------
mylis... | [
"def",
"filter_list",
"(",
"mylist",
",",
"bad_ixs",
")",
":",
"bad_ixs",
"=",
"sorted",
"(",
"bad_ixs",
",",
"reverse",
"=",
"True",
")",
"for",
"i",
"in",
"bad_ixs",
":",
"mylist",
".",
"pop",
"(",
"i",
")",
"return",
"mylist"
] | Removes indices from a list.
All elements in bad_ixs will be removed from the list.
Parameters
----------
mylist : list
list to filter out specific indices
bad_ixs : list of ints
indices to remove from list
Returns
-------
mylist : list
list with elements filte... | [
"Removes",
"indices",
"from",
"a",
"list",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L149-L171 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | rev_comp | def rev_comp(seq):
"""Get reverse complement of sequence.
rev_comp will maintain the case of the sequence.
Parameters
----------
seq : str
nucleotide sequence. valid {a, c, t, g, n}
Returns
-------
rev_comp_seq : str
reverse complement of sequence
"""
rev_seq =... | python | def rev_comp(seq):
"""Get reverse complement of sequence.
rev_comp will maintain the case of the sequence.
Parameters
----------
seq : str
nucleotide sequence. valid {a, c, t, g, n}
Returns
-------
rev_comp_seq : str
reverse complement of sequence
"""
rev_seq =... | [
"def",
"rev_comp",
"(",
"seq",
")",
":",
"rev_seq",
"=",
"seq",
"[",
":",
":",
"-",
"1",
"]",
"rev_comp_seq",
"=",
"''",
".",
"join",
"(",
"[",
"base_pairing",
"[",
"s",
"]",
"for",
"s",
"in",
"rev_seq",
"]",
")",
"return",
"rev_comp_seq"
] | Get reverse complement of sequence.
rev_comp will maintain the case of the sequence.
Parameters
----------
seq : str
nucleotide sequence. valid {a, c, t, g, n}
Returns
-------
rev_comp_seq : str
reverse complement of sequence | [
"Get",
"reverse",
"complement",
"of",
"sequence",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L174-L191 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | bed_generator | def bed_generator(bed_path):
"""Iterates through a BED file yielding parsed BED lines.
Parameters
----------
bed_path : str
path to BED file
Yields
------
BedLine(line) : BedLine
A BedLine object which has parsed the individual line in
a BED file.
"""
with o... | python | def bed_generator(bed_path):
"""Iterates through a BED file yielding parsed BED lines.
Parameters
----------
bed_path : str
path to BED file
Yields
------
BedLine(line) : BedLine
A BedLine object which has parsed the individual line in
a BED file.
"""
with o... | [
"def",
"bed_generator",
"(",
"bed_path",
")",
":",
"with",
"open",
"(",
"bed_path",
")",
"as",
"handle",
":",
"bed_reader",
"=",
"csv",
".",
"reader",
"(",
"handle",
",",
"delimiter",
"=",
"'\\t'",
")",
"for",
"line",
"in",
"bed_reader",
":",
"yield",
... | Iterates through a BED file yielding parsed BED lines.
Parameters
----------
bed_path : str
path to BED file
Yields
------
BedLine(line) : BedLine
A BedLine object which has parsed the individual line in
a BED file. | [
"Iterates",
"through",
"a",
"BED",
"file",
"yielding",
"parsed",
"BED",
"lines",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L212-L229 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | read_bed | def read_bed(file_path, restricted_genes=None):
"""Reads BED file and populates a dictionary separating genes
by chromosome.
Parameters
----------
file_path : str
path to BED file
filtered_genes: list
list of gene names to not use
Returns
-------
bed_dict: dict
... | python | def read_bed(file_path, restricted_genes=None):
"""Reads BED file and populates a dictionary separating genes
by chromosome.
Parameters
----------
file_path : str
path to BED file
filtered_genes: list
list of gene names to not use
Returns
-------
bed_dict: dict
... | [
"def",
"read_bed",
"(",
"file_path",
",",
"restricted_genes",
"=",
"None",
")",
":",
"bed_dict",
"=",
"OrderedDict",
"(",
")",
"for",
"bed_row",
"in",
"bed_generator",
"(",
"file_path",
")",
":",
"is_restrict_flag",
"=",
"restricted_genes",
"is",
"None",
"or",... | Reads BED file and populates a dictionary separating genes
by chromosome.
Parameters
----------
file_path : str
path to BED file
filtered_genes: list
list of gene names to not use
Returns
-------
bed_dict: dict
dictionary mapping chromosome keys to a list of BED... | [
"Reads",
"BED",
"file",
"and",
"populates",
"a",
"dictionary",
"separating",
"genes",
"by",
"chromosome",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L232-L257 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | _fix_mutation_df | def _fix_mutation_df(mutation_df, only_unique=False):
"""Drops invalid mutations and corrects for 1-based coordinates.
TODO: Be smarter about what coordinate system is put in the provided
mutations.
Parameters
----------
mutation_df : pd.DataFrame
user provided mutations
only_uniqu... | python | def _fix_mutation_df(mutation_df, only_unique=False):
"""Drops invalid mutations and corrects for 1-based coordinates.
TODO: Be smarter about what coordinate system is put in the provided
mutations.
Parameters
----------
mutation_df : pd.DataFrame
user provided mutations
only_uniqu... | [
"def",
"_fix_mutation_df",
"(",
"mutation_df",
",",
"only_unique",
"=",
"False",
")",
":",
"orig_len",
"=",
"len",
"(",
"mutation_df",
")",
"mutation_df",
"=",
"mutation_df",
"[",
"mutation_df",
".",
"Variant_Classification",
".",
"isin",
"(",
"variant_snv",
")"... | Drops invalid mutations and corrects for 1-based coordinates.
TODO: Be smarter about what coordinate system is put in the provided
mutations.
Parameters
----------
mutation_df : pd.DataFrame
user provided mutations
only_unique : bool
flag indicating whether only unique mutation... | [
"Drops",
"invalid",
"mutations",
"and",
"corrects",
"for",
"1",
"-",
"based",
"coordinates",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L260-L327 | train |
KarchinLab/probabilistic2020 | prob2020/python/utils.py | calc_windowed_sum | def calc_windowed_sum(aa_mut_pos,
germ_aa,
somatic_aa,
window=[3]):
"""Calculate the sum of mutations within a window around a particular mutated
codon.
Parameters
----------
aa_mut_pos : list
list of mutated amino acid posit... | python | def calc_windowed_sum(aa_mut_pos,
germ_aa,
somatic_aa,
window=[3]):
"""Calculate the sum of mutations within a window around a particular mutated
codon.
Parameters
----------
aa_mut_pos : list
list of mutated amino acid posit... | [
"def",
"calc_windowed_sum",
"(",
"aa_mut_pos",
",",
"germ_aa",
",",
"somatic_aa",
",",
"window",
"=",
"[",
"3",
"]",
")",
":",
"pos_ctr",
",",
"pos_sum",
"=",
"{",
"}",
",",
"{",
"w",
":",
"{",
"}",
"for",
"w",
"in",
"window",
"}",
"num_pos",
"=",
... | Calculate the sum of mutations within a window around a particular mutated
codon.
Parameters
----------
aa_mut_pos : list
list of mutated amino acid positions
germ_aa : list
Reference amino acid
somatic_aa : list
Somatic amino acid (if missense)
window : list
... | [
"Calculate",
"the",
"sum",
"of",
"mutations",
"within",
"a",
"window",
"around",
"a",
"particular",
"mutated",
"codon",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/utils.py#L359-L426 | train |
KarchinLab/probabilistic2020 | prob2020/python/mutation_context.py | get_all_context_names | def get_all_context_names(context_num):
"""Based on the nucleotide base context number, return
a list of strings representing each context.
Parameters
----------
context_num : int
number representing the amount of nucleotide base context to use.
Returns
-------
a list of st... | python | def get_all_context_names(context_num):
"""Based on the nucleotide base context number, return
a list of strings representing each context.
Parameters
----------
context_num : int
number representing the amount of nucleotide base context to use.
Returns
-------
a list of st... | [
"def",
"get_all_context_names",
"(",
"context_num",
")",
":",
"if",
"context_num",
"==",
"0",
":",
"return",
"[",
"'None'",
"]",
"elif",
"context_num",
"==",
"1",
":",
"return",
"[",
"'A'",
",",
"'C'",
",",
"'T'",
",",
"'G'",
"]",
"elif",
"context_num",
... | Based on the nucleotide base context number, return
a list of strings representing each context.
Parameters
----------
context_num : int
number representing the amount of nucleotide base context to use.
Returns
-------
a list of strings containing the names of the base contexts | [
"Based",
"on",
"the",
"nucleotide",
"base",
"context",
"number",
"return",
"a",
"list",
"of",
"strings",
"representing",
"each",
"context",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mutation_context.py#L18-L52 | train |
KarchinLab/probabilistic2020 | prob2020/python/mutation_context.py | get_chasm_context | def get_chasm_context(tri_nuc):
"""Returns the mutation context acording to CHASM.
For more information about CHASM's mutation context, look
at http://wiki.chasmsoftware.org/index.php/CHASM_Overview.
Essentially CHASM uses a few specified di-nucleotide contexts
followed by single nucleotide context... | python | def get_chasm_context(tri_nuc):
"""Returns the mutation context acording to CHASM.
For more information about CHASM's mutation context, look
at http://wiki.chasmsoftware.org/index.php/CHASM_Overview.
Essentially CHASM uses a few specified di-nucleotide contexts
followed by single nucleotide context... | [
"def",
"get_chasm_context",
"(",
"tri_nuc",
")",
":",
"if",
"len",
"(",
"tri_nuc",
")",
"!=",
"3",
":",
"raise",
"ValueError",
"(",
"'Chasm context requires a three nucleotide string '",
"'(Provided: \"{0}\")'",
".",
"format",
"(",
"tri_nuc",
")",
")",
"if",
"tri_... | Returns the mutation context acording to CHASM.
For more information about CHASM's mutation context, look
at http://wiki.chasmsoftware.org/index.php/CHASM_Overview.
Essentially CHASM uses a few specified di-nucleotide contexts
followed by single nucleotide context.
Parameters
----------
tr... | [
"Returns",
"the",
"mutation",
"context",
"acording",
"to",
"CHASM",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mutation_context.py#L117-L151 | train |
KarchinLab/probabilistic2020 | prob2020/python/mutation_context.py | get_aa_mut_info | def get_aa_mut_info(coding_pos, somatic_base, gene_seq):
"""Retrieves relevant information about the effect of a somatic
SNV on the amino acid of a gene.
Information includes the germline codon, somatic codon, codon
position, germline AA, and somatic AA.
Parameters
----------
coding_pos : ... | python | def get_aa_mut_info(coding_pos, somatic_base, gene_seq):
"""Retrieves relevant information about the effect of a somatic
SNV on the amino acid of a gene.
Information includes the germline codon, somatic codon, codon
position, germline AA, and somatic AA.
Parameters
----------
coding_pos : ... | [
"def",
"get_aa_mut_info",
"(",
"coding_pos",
",",
"somatic_base",
",",
"gene_seq",
")",
":",
"if",
"not",
"somatic_base",
":",
"aa_info",
"=",
"{",
"'Reference Codon'",
":",
"[",
"]",
",",
"'Somatic Codon'",
":",
"[",
"]",
",",
"'Codon Pos'",
":",
"[",
"]"... | Retrieves relevant information about the effect of a somatic
SNV on the amino acid of a gene.
Information includes the germline codon, somatic codon, codon
position, germline AA, and somatic AA.
Parameters
----------
coding_pos : iterable of ints
Contains the base position (0-based) of... | [
"Retrieves",
"relevant",
"information",
"about",
"the",
"effect",
"of",
"a",
"somatic",
"SNV",
"on",
"the",
"amino",
"acid",
"of",
"a",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/mutation_context.py#L196-L252 | train |
KarchinLab/probabilistic2020 | prob2020/python/process_result.py | handle_tsg_results | def handle_tsg_results(permutation_result):
"""Handles result from TSG results.
Takes in output from multiprocess_permutation function and converts to
a better formatted dataframe.
Parameters
----------
permutation_result : list
output from multiprocess_permutation
Returns
---... | python | def handle_tsg_results(permutation_result):
"""Handles result from TSG results.
Takes in output from multiprocess_permutation function and converts to
a better formatted dataframe.
Parameters
----------
permutation_result : list
output from multiprocess_permutation
Returns
---... | [
"def",
"handle_tsg_results",
"(",
"permutation_result",
")",
":",
"permutation_df",
"=",
"pd",
".",
"DataFrame",
"(",
"sorted",
"(",
"permutation_result",
",",
"key",
"=",
"lambda",
"x",
":",
"x",
"[",
"2",
"]",
"if",
"x",
"[",
"2",
"]",
"is",
"not",
"... | Handles result from TSG results.
Takes in output from multiprocess_permutation function and converts to
a better formatted dataframe.
Parameters
----------
permutation_result : list
output from multiprocess_permutation
Returns
-------
permutation_df : pd.DataFrame
form... | [
"Handles",
"result",
"from",
"TSG",
"results",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/process_result.py#L8-L45 | train |
KarchinLab/probabilistic2020 | scripts/calc_non_coding_frameshift_rate.py | get_frameshift_info | def get_frameshift_info(fs_df, bins):
"""Counts frameshifts stratified by a given length.
Parameters
----------
fs_df : pd.DataFrame
indel mutations from non-coding portion
bins : int
number of different length categories for frameshifts
Returns
-------
indel_len : list... | python | def get_frameshift_info(fs_df, bins):
"""Counts frameshifts stratified by a given length.
Parameters
----------
fs_df : pd.DataFrame
indel mutations from non-coding portion
bins : int
number of different length categories for frameshifts
Returns
-------
indel_len : list... | [
"def",
"get_frameshift_info",
"(",
"fs_df",
",",
"bins",
")",
":",
"fs_df",
"=",
"compute_indel_length",
"(",
"fs_df",
")",
"num_indels",
"=",
"[",
"]",
"indel_len",
"=",
"[",
"]",
"num_categories",
"=",
"0",
"i",
"=",
"1",
"while",
"(",
"num_categories",
... | Counts frameshifts stratified by a given length.
Parameters
----------
fs_df : pd.DataFrame
indel mutations from non-coding portion
bins : int
number of different length categories for frameshifts
Returns
-------
indel_len : list
length of specific frameshift length... | [
"Counts",
"frameshifts",
"stratified",
"by",
"a",
"given",
"length",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/scripts/calc_non_coding_frameshift_rate.py#L14-L49 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.set_mutation_type | def set_mutation_type(self, mut_type=''):
"""Sets the mutation type attribute to a single label based on
attribute flags.
Kwargs:
mut_type (str): value to set self.mut_type
"""
if mut_type:
# user specifies a mutation type
self.mutation_type =... | python | def set_mutation_type(self, mut_type=''):
"""Sets the mutation type attribute to a single label based on
attribute flags.
Kwargs:
mut_type (str): value to set self.mut_type
"""
if mut_type:
# user specifies a mutation type
self.mutation_type =... | [
"def",
"set_mutation_type",
"(",
"self",
",",
"mut_type",
"=",
"''",
")",
":",
"if",
"mut_type",
":",
"self",
".",
"mutation_type",
"=",
"mut_type",
"else",
":",
"if",
"not",
"self",
".",
"is_valid",
":",
"self",
".",
"mutation_type",
"=",
"'not valid'",
... | Sets the mutation type attribute to a single label based on
attribute flags.
Kwargs:
mut_type (str): value to set self.mut_type | [
"Sets",
"the",
"mutation",
"type",
"attribute",
"to",
"a",
"single",
"label",
"based",
"on",
"attribute",
"flags",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L52-L93 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.set_amino_acid | def set_amino_acid(self, aa):
"""Set amino acid change and position."""
aa = aa.upper() # make sure it is upper case
aa = aa[2:] if aa.startswith('P.') else aa # strip "p."
self.__set_mutation_status() # set flags detailing the type of mutation
self.__parse_hgvs_syntax(aa) | python | def set_amino_acid(self, aa):
"""Set amino acid change and position."""
aa = aa.upper() # make sure it is upper case
aa = aa[2:] if aa.startswith('P.') else aa # strip "p."
self.__set_mutation_status() # set flags detailing the type of mutation
self.__parse_hgvs_syntax(aa) | [
"def",
"set_amino_acid",
"(",
"self",
",",
"aa",
")",
":",
"aa",
"=",
"aa",
".",
"upper",
"(",
")",
"aa",
"=",
"aa",
"[",
"2",
":",
"]",
"if",
"aa",
".",
"startswith",
"(",
"'P.'",
")",
"else",
"aa",
"self",
".",
"__set_mutation_status",
"(",
")"... | Set amino acid change and position. | [
"Set",
"amino",
"acid",
"change",
"and",
"position",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L98-L103 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_missense_status | def __set_missense_status(self, hgvs_string):
"""Sets the self.is_missense flag."""
# set missense status
if re.search('^[A-Z?]\d+[A-Z?]$', hgvs_string):
self.is_missense = True
self.is_non_silent = True
else:
self.is_missense = False | python | def __set_missense_status(self, hgvs_string):
"""Sets the self.is_missense flag."""
# set missense status
if re.search('^[A-Z?]\d+[A-Z?]$', hgvs_string):
self.is_missense = True
self.is_non_silent = True
else:
self.is_missense = False | [
"def",
"__set_missense_status",
"(",
"self",
",",
"hgvs_string",
")",
":",
"if",
"re",
".",
"search",
"(",
"'^[A-Z?]\\d+[A-Z?]$'",
",",
"hgvs_string",
")",
":",
"self",
".",
"is_missense",
"=",
"True",
"self",
".",
"is_non_silent",
"=",
"True",
"else",
":",
... | Sets the self.is_missense flag. | [
"Sets",
"the",
"self",
".",
"is_missense",
"flag",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L127-L134 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_lost_start_status | def __set_lost_start_status(self, hgvs_string):
"""Sets the self.is_lost_start flag."""
# set is lost start status
mymatch = re.search('^([A-Z?])(\d+)([A-Z?])$', hgvs_string)
if mymatch:
grps = mymatch.groups()
if int(grps[1]) == 1 and grps[0] != grps[2]:
... | python | def __set_lost_start_status(self, hgvs_string):
"""Sets the self.is_lost_start flag."""
# set is lost start status
mymatch = re.search('^([A-Z?])(\d+)([A-Z?])$', hgvs_string)
if mymatch:
grps = mymatch.groups()
if int(grps[1]) == 1 and grps[0] != grps[2]:
... | [
"def",
"__set_lost_start_status",
"(",
"self",
",",
"hgvs_string",
")",
":",
"mymatch",
"=",
"re",
".",
"search",
"(",
"'^([A-Z?])(\\d+)([A-Z?])$'",
",",
"hgvs_string",
")",
"if",
"mymatch",
":",
"grps",
"=",
"mymatch",
".",
"groups",
"(",
")",
"if",
"int",
... | Sets the self.is_lost_start flag. | [
"Sets",
"the",
"self",
".",
"is_lost_start",
"flag",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L136-L148 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_frame_shift_status | def __set_frame_shift_status(self):
"""Check for frame shift and set the self.is_frame_shift flag."""
if 'fs' in self.hgvs_original:
self.is_frame_shift = True
self.is_non_silent = True
elif re.search('[A-Z]\d+[A-Z]+\*', self.hgvs_original):
# it looks like so... | python | def __set_frame_shift_status(self):
"""Check for frame shift and set the self.is_frame_shift flag."""
if 'fs' in self.hgvs_original:
self.is_frame_shift = True
self.is_non_silent = True
elif re.search('[A-Z]\d+[A-Z]+\*', self.hgvs_original):
# it looks like so... | [
"def",
"__set_frame_shift_status",
"(",
"self",
")",
":",
"if",
"'fs'",
"in",
"self",
".",
"hgvs_original",
":",
"self",
".",
"is_frame_shift",
"=",
"True",
"self",
".",
"is_non_silent",
"=",
"True",
"elif",
"re",
".",
"search",
"(",
"'[A-Z]\\d+[A-Z]+\\*'",
... | Check for frame shift and set the self.is_frame_shift flag. | [
"Check",
"for",
"frame",
"shift",
"and",
"set",
"the",
"self",
".",
"is_frame_shift",
"flag",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L150-L161 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_lost_stop_status | def __set_lost_stop_status(self, hgvs_string):
"""Check if the stop codon was mutated to something other than
a stop codon."""
lost_stop_pattern = '^\*\d+[A-Z?]+\*?$'
if re.search(lost_stop_pattern, hgvs_string):
self.is_lost_stop = True
self.is_non_silent = True
... | python | def __set_lost_stop_status(self, hgvs_string):
"""Check if the stop codon was mutated to something other than
a stop codon."""
lost_stop_pattern = '^\*\d+[A-Z?]+\*?$'
if re.search(lost_stop_pattern, hgvs_string):
self.is_lost_stop = True
self.is_non_silent = True
... | [
"def",
"__set_lost_stop_status",
"(",
"self",
",",
"hgvs_string",
")",
":",
"lost_stop_pattern",
"=",
"'^\\*\\d+[A-Z?]+\\*?$'",
"if",
"re",
".",
"search",
"(",
"lost_stop_pattern",
",",
"hgvs_string",
")",
":",
"self",
".",
"is_lost_stop",
"=",
"True",
"self",
"... | Check if the stop codon was mutated to something other than
a stop codon. | [
"Check",
"if",
"the",
"stop",
"codon",
"was",
"mutated",
"to",
"something",
"other",
"than",
"a",
"stop",
"codon",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L163-L171 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_premature_stop_codon_status | def __set_premature_stop_codon_status(self, hgvs_string):
"""Set whether there is a premature stop codon."""
if re.search('.+\*(\d+)?$', hgvs_string):
self.is_premature_stop_codon = True
self.is_non_silent = True
# check if it is also a nonsense mutation
... | python | def __set_premature_stop_codon_status(self, hgvs_string):
"""Set whether there is a premature stop codon."""
if re.search('.+\*(\d+)?$', hgvs_string):
self.is_premature_stop_codon = True
self.is_non_silent = True
# check if it is also a nonsense mutation
... | [
"def",
"__set_premature_stop_codon_status",
"(",
"self",
",",
"hgvs_string",
")",
":",
"if",
"re",
".",
"search",
"(",
"'.+\\*(\\d+)?$'",
",",
"hgvs_string",
")",
":",
"self",
".",
"is_premature_stop_codon",
"=",
"True",
"self",
".",
"is_non_silent",
"=",
"True"... | Set whether there is a premature stop codon. | [
"Set",
"whether",
"there",
"is",
"a",
"premature",
"stop",
"codon",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L173-L186 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_indel_status | def __set_indel_status(self):
"""Sets flags related to the mutation being an indel."""
# set indel status
if "ins" in self.hgvs_original:
# mutation is insertion
self.is_insertion = True
self.is_deletion = False
self.is_indel = True
sel... | python | def __set_indel_status(self):
"""Sets flags related to the mutation being an indel."""
# set indel status
if "ins" in self.hgvs_original:
# mutation is insertion
self.is_insertion = True
self.is_deletion = False
self.is_indel = True
sel... | [
"def",
"__set_indel_status",
"(",
"self",
")",
":",
"if",
"\"ins\"",
"in",
"self",
".",
"hgvs_original",
":",
"self",
".",
"is_insertion",
"=",
"True",
"self",
".",
"is_deletion",
"=",
"False",
"self",
".",
"is_indel",
"=",
"True",
"self",
".",
"is_non_sil... | Sets flags related to the mutation being an indel. | [
"Sets",
"flags",
"related",
"to",
"the",
"mutation",
"being",
"an",
"indel",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L188-L207 | train |
KarchinLab/probabilistic2020 | prob2020/python/amino_acid.py | AminoAcid.__set_unkown_effect | def __set_unkown_effect(self, hgvs_string):
"""Sets a flag for unkown effect according to HGVS syntax. The
COSMIC database also uses unconventional questionmarks to denote
missing information.
Args:
hgvs_string (str): hgvs syntax with "p." removed
"""
# Stand... | python | def __set_unkown_effect(self, hgvs_string):
"""Sets a flag for unkown effect according to HGVS syntax. The
COSMIC database also uses unconventional questionmarks to denote
missing information.
Args:
hgvs_string (str): hgvs syntax with "p." removed
"""
# Stand... | [
"def",
"__set_unkown_effect",
"(",
"self",
",",
"hgvs_string",
")",
":",
"unknown_effect_list",
"=",
"[",
"'?'",
",",
"'(=)'",
",",
"'='",
"]",
"if",
"hgvs_string",
"in",
"unknown_effect_list",
":",
"self",
".",
"unknown_effect",
"=",
"True",
"elif",
"\"(\"",
... | Sets a flag for unkown effect according to HGVS syntax. The
COSMIC database also uses unconventional questionmarks to denote
missing information.
Args:
hgvs_string (str): hgvs syntax with "p." removed | [
"Sets",
"a",
"flag",
"for",
"unkown",
"effect",
"according",
"to",
"HGVS",
"syntax",
".",
"The",
"COSMIC",
"database",
"also",
"uses",
"unconventional",
"questionmarks",
"to",
"denote",
"missing",
"information",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/amino_acid.py#L209-L233 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | deleterious_permutation | def deleterious_permutation(obs_del,
context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
stop_criteria=100,
... | python | def deleterious_permutation(obs_del,
context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
stop_criteria=100,
... | [
"def",
"deleterious_permutation",
"(",
"obs_del",
",",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"num_permutations",
"=",
"10000",
",",
"stop_criteria",
"=",
"100",
",",
"pseudo_count",
"=",
"0",
",",
"max_batch",
"=",
"2... | Performs null-permutations for deleterious mutation statistics
in a single gene.
Parameters
----------
context_counts : pd.Series
number of mutations for each context
context_to_mut : dict
dictionary mapping nucleotide context to a list of observed
somatic base changes.
... | [
"Performs",
"null",
"-",
"permutations",
"for",
"deleterious",
"mutation",
"statistics",
"in",
"a",
"single",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L9-L96 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | protein_permutation | def protein_permutation(graph_score,
num_codons_obs,
context_counts,
context_to_mut,
seq_context,
gene_seq,
gene_graph,
num_permutations=10000,
... | python | def protein_permutation(graph_score,
num_codons_obs,
context_counts,
context_to_mut,
seq_context,
gene_seq,
gene_graph,
num_permutations=10000,
... | [
"def",
"protein_permutation",
"(",
"graph_score",
",",
"num_codons_obs",
",",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"gene_graph",
",",
"num_permutations",
"=",
"10000",
",",
"stop_criteria",
"=",
"100",
",",
"pseudo_count... | Performs null-simulations for position-based mutation statistics
in a single gene.
Parameters
----------
graph_score : float
clustering score for observed data
num_codons_obs : int
number of codons with missense mutation in observed data
context_counts : pd.Series
number... | [
"Performs",
"null",
"-",
"simulations",
"for",
"position",
"-",
"based",
"mutation",
"statistics",
"in",
"a",
"single",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L360-L483 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | effect_permutation | def effect_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
pseudo_count=0):
"""Performs null-permutations for effect-based mutation statistics
in a single... | python | def effect_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
pseudo_count=0):
"""Performs null-permutations for effect-based mutation statistics
in a single... | [
"def",
"effect_permutation",
"(",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"num_permutations",
"=",
"10000",
",",
"pseudo_count",
"=",
"0",
")",
":",
"mycontexts",
"=",
"context_counts",
".",
"index",
".",
"tolist",
"(",... | Performs null-permutations for effect-based mutation statistics
in a single gene.
Parameters
----------
context_counts : pd.Series
number of mutations for each context
context_to_mut : dict
dictionary mapping nucleotide context to a list of observed
somatic base changes.
... | [
"Performs",
"null",
"-",
"permutations",
"for",
"effect",
"-",
"based",
"mutation",
"statistics",
"in",
"a",
"single",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L486-L552 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | non_silent_ratio_permutation | def non_silent_ratio_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000):
"""Performs null-permutations for non-silent ratio across all genes.
... | python | def non_silent_ratio_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000):
"""Performs null-permutations for non-silent ratio across all genes.
... | [
"def",
"non_silent_ratio_permutation",
"(",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"num_permutations",
"=",
"10000",
")",
":",
"mycontexts",
"=",
"context_counts",
".",
"index",
".",
"tolist",
"(",
")",
"somatic_base",
"... | Performs null-permutations for non-silent ratio across all genes.
Parameters
----------
context_counts : pd.Series
number of mutations for each context
context_to_mut : dict
dictionary mapping nucleotide context to a list of observed
somatic base changes.
seq_context : Seque... | [
"Performs",
"null",
"-",
"permutations",
"for",
"non",
"-",
"silent",
"ratio",
"across",
"all",
"genes",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L555-L606 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | summary_permutation | def summary_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
score_dir,
num_permutations=10000,
min_frac=0.0,
min_recur=2,
... | python | def summary_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
score_dir,
num_permutations=10000,
min_frac=0.0,
min_recur=2,
... | [
"def",
"summary_permutation",
"(",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"score_dir",
",",
"num_permutations",
"=",
"10000",
",",
"min_frac",
"=",
"0.0",
",",
"min_recur",
"=",
"2",
",",
"drop_silent",
"=",
"False",
... | Performs null-permutations and summarizes the results as features over
the gene.
Parameters
----------
context_counts : pd.Series
number of mutations for each context
context_to_mut : dict
dictionary mapping nucleotide context to a list of observed
somatic base changes.
... | [
"Performs",
"null",
"-",
"permutations",
"and",
"summarizes",
"the",
"results",
"as",
"features",
"over",
"the",
"gene",
"."
] | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L609-L686 | train |
KarchinLab/probabilistic2020 | prob2020/python/permutation.py | maf_permutation | def maf_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
drop_silent=False):
"""Performs null-permutations across all genes and records the results in
a format like a MAF... | python | def maf_permutation(context_counts,
context_to_mut,
seq_context,
gene_seq,
num_permutations=10000,
drop_silent=False):
"""Performs null-permutations across all genes and records the results in
a format like a MAF... | [
"def",
"maf_permutation",
"(",
"context_counts",
",",
"context_to_mut",
",",
"seq_context",
",",
"gene_seq",
",",
"num_permutations",
"=",
"10000",
",",
"drop_silent",
"=",
"False",
")",
":",
"mycontexts",
"=",
"context_counts",
".",
"index",
".",
"tolist",
"(",... | Performs null-permutations across all genes and records the results in
a format like a MAF file. This could be useful for examining the null
permutations because the alternative approaches always summarize the results.
With the simulated null-permutations, novel metrics can be applied to create
an empir... | [
"Performs",
"null",
"-",
"permutations",
"across",
"all",
"genes",
"and",
"records",
"the",
"results",
"in",
"a",
"format",
"like",
"a",
"MAF",
"file",
".",
"This",
"could",
"be",
"useful",
"for",
"examining",
"the",
"null",
"permutations",
"because",
"the",... | 5d70583b0a7c07cfe32e95f3a70e05df412acb84 | https://github.com/KarchinLab/probabilistic2020/blob/5d70583b0a7c07cfe32e95f3a70e05df412acb84/prob2020/python/permutation.py#L689-L783 | train |
sv0/django-markdown-app | django_markdown/utils.py | editor_js_initialization | def editor_js_initialization(selector, **extra_settings):
""" Return script tag with initialization code. """
init_template = loader.get_template(
settings.MARKDOWN_EDITOR_INIT_TEMPLATE)
options = dict(
previewParserPath=reverse('django_markdown_preview'),
**settings.MARKDOWN_EDITO... | python | def editor_js_initialization(selector, **extra_settings):
""" Return script tag with initialization code. """
init_template = loader.get_template(
settings.MARKDOWN_EDITOR_INIT_TEMPLATE)
options = dict(
previewParserPath=reverse('django_markdown_preview'),
**settings.MARKDOWN_EDITO... | [
"def",
"editor_js_initialization",
"(",
"selector",
",",
"**",
"extra_settings",
")",
":",
"init_template",
"=",
"loader",
".",
"get_template",
"(",
"settings",
".",
"MARKDOWN_EDITOR_INIT_TEMPLATE",
")",
"options",
"=",
"dict",
"(",
"previewParserPath",
"=",
"revers... | Return script tag with initialization code. | [
"Return",
"script",
"tag",
"with",
"initialization",
"code",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/utils.py#L42-L56 | train |
sv0/django-markdown-app | django_markdown/views.py | preview | def preview(request):
""" Render preview page.
:returns: A rendered preview
"""
if settings.MARKDOWN_PROTECT_PREVIEW:
user = getattr(request, 'user', None)
if not user or not user.is_staff:
from django.contrib.auth.views import redirect_to_login
return redirect_... | python | def preview(request):
""" Render preview page.
:returns: A rendered preview
"""
if settings.MARKDOWN_PROTECT_PREVIEW:
user = getattr(request, 'user', None)
if not user or not user.is_staff:
from django.contrib.auth.views import redirect_to_login
return redirect_... | [
"def",
"preview",
"(",
"request",
")",
":",
"if",
"settings",
".",
"MARKDOWN_PROTECT_PREVIEW",
":",
"user",
"=",
"getattr",
"(",
"request",
",",
"'user'",
",",
"None",
")",
"if",
"not",
"user",
"or",
"not",
"user",
".",
"is_staff",
":",
"from",
"django",... | Render preview page.
:returns: A rendered preview | [
"Render",
"preview",
"page",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/views.py#L7-L23 | train |
sv0/django-markdown-app | django_markdown/flatpages.py | register | def register():
""" Register markdown for flatpages. """
admin.site.unregister(FlatPage)
admin.site.register(FlatPage, LocalFlatPageAdmin) | python | def register():
""" Register markdown for flatpages. """
admin.site.unregister(FlatPage)
admin.site.register(FlatPage, LocalFlatPageAdmin) | [
"def",
"register",
"(",
")",
":",
"admin",
".",
"site",
".",
"unregister",
"(",
"FlatPage",
")",
"admin",
".",
"site",
".",
"register",
"(",
"FlatPage",
",",
"LocalFlatPageAdmin",
")"
] | Register markdown for flatpages. | [
"Register",
"markdown",
"for",
"flatpages",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/flatpages.py#L25-L29 | train |
sv0/django-markdown-app | django_markdown/templatetags/django_markdown.py | markdown_editor | def markdown_editor(selector):
""" Enable markdown editor for given textarea.
:returns: Editor template context.
"""
return dict(
selector=selector,
extra_settings=mark_safe(simplejson.dumps(
dict(previewParserPath=reverse('django_markdown_preview'))))) | python | def markdown_editor(selector):
""" Enable markdown editor for given textarea.
:returns: Editor template context.
"""
return dict(
selector=selector,
extra_settings=mark_safe(simplejson.dumps(
dict(previewParserPath=reverse('django_markdown_preview'))))) | [
"def",
"markdown_editor",
"(",
"selector",
")",
":",
"return",
"dict",
"(",
"selector",
"=",
"selector",
",",
"extra_settings",
"=",
"mark_safe",
"(",
"simplejson",
".",
"dumps",
"(",
"dict",
"(",
"previewParserPath",
"=",
"reverse",
"(",
"'django_markdown_previ... | Enable markdown editor for given textarea.
:returns: Editor template context. | [
"Enable",
"markdown",
"editor",
"for",
"given",
"textarea",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/templatetags/django_markdown.py#L57-L66 | train |
sv0/django-markdown-app | django_markdown/templatetags/django_markdown.py | markdown_media_css | def markdown_media_css():
""" Add css requirements to HTML.
:returns: Editor template context.
"""
return dict(
CSS_SET=posixpath.join(
settings.MARKDOWN_SET_PATH, settings.MARKDOWN_SET_NAME, 'style.css'
),
CSS_SKIN=posixpath.join(
'django_markdown', 'sk... | python | def markdown_media_css():
""" Add css requirements to HTML.
:returns: Editor template context.
"""
return dict(
CSS_SET=posixpath.join(
settings.MARKDOWN_SET_PATH, settings.MARKDOWN_SET_NAME, 'style.css'
),
CSS_SKIN=posixpath.join(
'django_markdown', 'sk... | [
"def",
"markdown_media_css",
"(",
")",
":",
"return",
"dict",
"(",
"CSS_SET",
"=",
"posixpath",
".",
"join",
"(",
"settings",
".",
"MARKDOWN_SET_PATH",
",",
"settings",
".",
"MARKDOWN_SET_NAME",
",",
"'style.css'",
")",
",",
"CSS_SKIN",
"=",
"posixpath",
".",
... | Add css requirements to HTML.
:returns: Editor template context. | [
"Add",
"css",
"requirements",
"to",
"HTML",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/templatetags/django_markdown.py#L96-L110 | train |
sv0/django-markdown-app | django_markdown/pypandoc.py | convert | def convert(source, to, format=None, extra_args=(), encoding='utf-8'):
"""Convert given `source` from `format` `to` another.
`source` may be either a file path or a string to be converted.
It's possible to pass `extra_args` if needed. In case `format` is not
provided, it will try to invert the format ... | python | def convert(source, to, format=None, extra_args=(), encoding='utf-8'):
"""Convert given `source` from `format` `to` another.
`source` may be either a file path or a string to be converted.
It's possible to pass `extra_args` if needed. In case `format` is not
provided, it will try to invert the format ... | [
"def",
"convert",
"(",
"source",
",",
"to",
",",
"format",
"=",
"None",
",",
"extra_args",
"=",
"(",
")",
",",
"encoding",
"=",
"'utf-8'",
")",
":",
"return",
"_convert",
"(",
"_read_file",
",",
"_process_file",
",",
"source",
",",
"to",
",",
"format",... | Convert given `source` from `format` `to` another.
`source` may be either a file path or a string to be converted.
It's possible to pass `extra_args` if needed. In case `format` is not
provided, it will try to invert the format based on given `source`.
Raises OSError if pandoc is not found! Make sure... | [
"Convert",
"given",
"source",
"from",
"format",
"to",
"another",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/pypandoc.py#L13-L28 | train |
sv0/django-markdown-app | django_markdown/pypandoc.py | get_pandoc_formats | def get_pandoc_formats():
""" Dynamic preprocessor for Pandoc formats.
Return 2 lists. "from_formats" and "to_formats".
"""
try:
p = subprocess.Popen(
['pandoc', '-h'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
except OSError:
raise OSError("... | python | def get_pandoc_formats():
""" Dynamic preprocessor for Pandoc formats.
Return 2 lists. "from_formats" and "to_formats".
"""
try:
p = subprocess.Popen(
['pandoc', '-h'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
except OSError:
raise OSError("... | [
"def",
"get_pandoc_formats",
"(",
")",
":",
"try",
":",
"p",
"=",
"subprocess",
".",
"Popen",
"(",
"[",
"'pandoc'",
",",
"'-h'",
"]",
",",
"stdin",
"=",
"subprocess",
".",
"PIPE",
",",
"stdout",
"=",
"subprocess",
".",
"PIPE",
")",
"except",
"OSError",... | Dynamic preprocessor for Pandoc formats.
Return 2 lists. "from_formats" and "to_formats". | [
"Dynamic",
"preprocessor",
"for",
"Pandoc",
"formats",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/pypandoc.py#L89-L109 | train |
sv0/django-markdown-app | django_markdown/widgets.py | MarkdownWidget.render | def render(self, name, value, attrs=None, renderer=None):
""" Render widget.
:returns: A rendered HTML
"""
html = super(MarkdownWidget, self).render(name, value, attrs, renderer)
attrs = self.build_attrs(attrs)
html += editor_js_initialization("#%s" % attrs['id'])
... | python | def render(self, name, value, attrs=None, renderer=None):
""" Render widget.
:returns: A rendered HTML
"""
html = super(MarkdownWidget, self).render(name, value, attrs, renderer)
attrs = self.build_attrs(attrs)
html += editor_js_initialization("#%s" % attrs['id'])
... | [
"def",
"render",
"(",
"self",
",",
"name",
",",
"value",
",",
"attrs",
"=",
"None",
",",
"renderer",
"=",
"None",
")",
":",
"html",
"=",
"super",
"(",
"MarkdownWidget",
",",
"self",
")",
".",
"render",
"(",
"name",
",",
"value",
",",
"attrs",
",",
... | Render widget.
:returns: A rendered HTML | [
"Render",
"widget",
"."
] | 973968c68d79cbe35304e9d6da876ad33f427d2d | https://github.com/sv0/django-markdown-app/blob/973968c68d79cbe35304e9d6da876ad33f427d2d/django_markdown/widgets.py#L29-L38 | train |
sprin/markdown-inline-graphviz | mdx_inline_graphviz.py | InlineGraphvizExtension.extendMarkdown | def extendMarkdown(self, md, md_globals):
""" Add InlineGraphvizPreprocessor to the Markdown instance. """
md.registerExtension(self)
md.preprocessors.add('graphviz_block',
InlineGraphvizPreprocessor(md),
"_begin") | python | def extendMarkdown(self, md, md_globals):
""" Add InlineGraphvizPreprocessor to the Markdown instance. """
md.registerExtension(self)
md.preprocessors.add('graphviz_block',
InlineGraphvizPreprocessor(md),
"_begin") | [
"def",
"extendMarkdown",
"(",
"self",
",",
"md",
",",
"md_globals",
")",
":",
"md",
".",
"registerExtension",
"(",
"self",
")",
"md",
".",
"preprocessors",
".",
"add",
"(",
"'graphviz_block'",
",",
"InlineGraphvizPreprocessor",
"(",
"md",
")",
",",
"\"_begin... | Add InlineGraphvizPreprocessor to the Markdown instance. | [
"Add",
"InlineGraphvizPreprocessor",
"to",
"the",
"Markdown",
"instance",
"."
] | 9664863b3002d88243c9ee5e14c195e037e54618 | https://github.com/sprin/markdown-inline-graphviz/blob/9664863b3002d88243c9ee5e14c195e037e54618/mdx_inline_graphviz.py#L38-L44 | train |
sprin/markdown-inline-graphviz | mdx_inline_graphviz.py | InlineGraphvizPreprocessor.run | def run(self, lines):
""" Match and generate dot code blocks."""
text = "\n".join(lines)
while 1:
m = BLOCK_RE.search(text)
if m:
command = m.group('command')
# Whitelist command, prevent command injection.
if command not i... | python | def run(self, lines):
""" Match and generate dot code blocks."""
text = "\n".join(lines)
while 1:
m = BLOCK_RE.search(text)
if m:
command = m.group('command')
# Whitelist command, prevent command injection.
if command not i... | [
"def",
"run",
"(",
"self",
",",
"lines",
")",
":",
"text",
"=",
"\"\\n\"",
".",
"join",
"(",
"lines",
")",
"while",
"1",
":",
"m",
"=",
"BLOCK_RE",
".",
"search",
"(",
"text",
")",
"if",
"m",
":",
"command",
"=",
"m",
".",
"group",
"(",
"'comma... | Match and generate dot code blocks. | [
"Match",
"and",
"generate",
"dot",
"code",
"blocks",
"."
] | 9664863b3002d88243c9ee5e14c195e037e54618 | https://github.com/sprin/markdown-inline-graphviz/blob/9664863b3002d88243c9ee5e14c195e037e54618/mdx_inline_graphviz.py#L52-L104 | train |
zabuldon/teslajsonpy | teslajsonpy/connection.py | Connection.post | def post(self, command, data=None):
"""Post data to API."""
now = calendar.timegm(datetime.datetime.now().timetuple())
if now > self.expiration:
auth = self.__open("/oauth/token", data=self.oauth)
self.__sethead(auth['access_token'])
return self.__open("%s%s" % (s... | python | def post(self, command, data=None):
"""Post data to API."""
now = calendar.timegm(datetime.datetime.now().timetuple())
if now > self.expiration:
auth = self.__open("/oauth/token", data=self.oauth)
self.__sethead(auth['access_token'])
return self.__open("%s%s" % (s... | [
"def",
"post",
"(",
"self",
",",
"command",
",",
"data",
"=",
"None",
")",
":",
"now",
"=",
"calendar",
".",
"timegm",
"(",
"datetime",
".",
"datetime",
".",
"now",
"(",
")",
".",
"timetuple",
"(",
")",
")",
"if",
"now",
">",
"self",
".",
"expira... | Post data to API. | [
"Post",
"data",
"to",
"API",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/connection.py#L49-L56 | train |
zabuldon/teslajsonpy | teslajsonpy/connection.py | Connection.__sethead | def __sethead(self, access_token):
"""Set HTTP header."""
self.access_token = access_token
now = calendar.timegm(datetime.datetime.now().timetuple())
self.expiration = now + 1800
self.head = {"Authorization": "Bearer %s" % access_token,
"User-Agent": self.use... | python | def __sethead(self, access_token):
"""Set HTTP header."""
self.access_token = access_token
now = calendar.timegm(datetime.datetime.now().timetuple())
self.expiration = now + 1800
self.head = {"Authorization": "Bearer %s" % access_token,
"User-Agent": self.use... | [
"def",
"__sethead",
"(",
"self",
",",
"access_token",
")",
":",
"self",
".",
"access_token",
"=",
"access_token",
"now",
"=",
"calendar",
".",
"timegm",
"(",
"datetime",
".",
"datetime",
".",
"now",
"(",
")",
".",
"timetuple",
"(",
")",
")",
"self",
".... | Set HTTP header. | [
"Set",
"HTTP",
"header",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/connection.py#L58-L65 | train |
zabuldon/teslajsonpy | teslajsonpy/connection.py | Connection.__open | def __open(self, url, headers=None, data=None, baseurl=""):
"""Use raw urlopen command."""
headers = headers or {}
if not baseurl:
baseurl = self.baseurl
req = Request("%s%s" % (baseurl, url), headers=headers)
_LOGGER.debug(url)
try:
req.data = ur... | python | def __open(self, url, headers=None, data=None, baseurl=""):
"""Use raw urlopen command."""
headers = headers or {}
if not baseurl:
baseurl = self.baseurl
req = Request("%s%s" % (baseurl, url), headers=headers)
_LOGGER.debug(url)
try:
req.data = ur... | [
"def",
"__open",
"(",
"self",
",",
"url",
",",
"headers",
"=",
"None",
",",
"data",
"=",
"None",
",",
"baseurl",
"=",
"\"\"",
")",
":",
"headers",
"=",
"headers",
"or",
"{",
"}",
"if",
"not",
"baseurl",
":",
"baseurl",
"=",
"self",
".",
"baseurl",
... | Use raw urlopen command. | [
"Use",
"raw",
"urlopen",
"command",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/connection.py#L67-L92 | train |
zabuldon/teslajsonpy | teslajsonpy/binary_sensor.py | ParkingSensor.update | def update(self):
"""Update the parking brake sensor."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_drive_params(self._id)
if data:
if not data['shift_state'] or data['shift_state'] == 'P':
self.__state = True
... | python | def update(self):
"""Update the parking brake sensor."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_drive_params(self._id)
if data:
if not data['shift_state'] or data['shift_state'] == 'P':
self.__state = True
... | [
"def",
"update",
"(",
"self",
")",
":",
"self",
".",
"_controller",
".",
"update",
"(",
"self",
".",
"_id",
",",
"wake_if_asleep",
"=",
"False",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"get_drive_params",
"(",
"self",
".",
"_id",
")",
"if",
... | Update the parking brake sensor. | [
"Update",
"the",
"parking",
"brake",
"sensor",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/binary_sensor.py#L48-L56 | train |
zabuldon/teslajsonpy | teslajsonpy/climate.py | Climate.update | def update(self):
"""Update the HVAC state."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_climate_params(self._id)
if data:
if time.time() - self.__manual_update_time > 60:
self.__is_auto_conditioning_on = (data
... | python | def update(self):
"""Update the HVAC state."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_climate_params(self._id)
if data:
if time.time() - self.__manual_update_time > 60:
self.__is_auto_conditioning_on = (data
... | [
"def",
"update",
"(",
"self",
")",
":",
"self",
".",
"_controller",
".",
"update",
"(",
"self",
".",
"_id",
",",
"wake_if_asleep",
"=",
"False",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"get_climate_params",
"(",
"self",
".",
"_id",
")",
"if"... | Update the HVAC state. | [
"Update",
"the",
"HVAC",
"state",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/climate.py#L76-L98 | train |
zabuldon/teslajsonpy | teslajsonpy/climate.py | Climate.set_temperature | def set_temperature(self, temp):
"""Set both the driver and passenger temperature to temp."""
temp = round(temp, 1)
self.__manual_update_time = time.time()
data = self._controller.command(self._id, 'set_temps',
{"driver_temp": temp,
... | python | def set_temperature(self, temp):
"""Set both the driver and passenger temperature to temp."""
temp = round(temp, 1)
self.__manual_update_time = time.time()
data = self._controller.command(self._id, 'set_temps',
{"driver_temp": temp,
... | [
"def",
"set_temperature",
"(",
"self",
",",
"temp",
")",
":",
"temp",
"=",
"round",
"(",
"temp",
",",
"1",
")",
"self",
".",
"__manual_update_time",
"=",
"time",
".",
"time",
"(",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"se... | Set both the driver and passenger temperature to temp. | [
"Set",
"both",
"the",
"driver",
"and",
"passenger",
"temperature",
"to",
"temp",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/climate.py#L100-L110 | train |
zabuldon/teslajsonpy | teslajsonpy/climate.py | Climate.set_status | def set_status(self, enabled):
"""Enable or disable the HVAC."""
self.__manual_update_time = time.time()
if enabled:
data = self._controller.command(self._id,
'auto_conditioning_start',
wake_if_as... | python | def set_status(self, enabled):
"""Enable or disable the HVAC."""
self.__manual_update_time = time.time()
if enabled:
data = self._controller.command(self._id,
'auto_conditioning_start',
wake_if_as... | [
"def",
"set_status",
"(",
"self",
",",
"enabled",
")",
":",
"self",
".",
"__manual_update_time",
"=",
"time",
".",
"time",
"(",
")",
"if",
"enabled",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'auto_con... | Enable or disable the HVAC. | [
"Enable",
"or",
"disable",
"the",
"HVAC",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/climate.py#L112-L129 | train |
zabuldon/teslajsonpy | teslajsonpy/climate.py | TempSensor.update | def update(self):
"""Update the temperature."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_climate_params(self._id)
if data:
self.__inside_temp = (data['inside_temp'] if data['inside_temp']
else self._... | python | def update(self):
"""Update the temperature."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_climate_params(self._id)
if data:
self.__inside_temp = (data['inside_temp'] if data['inside_temp']
else self._... | [
"def",
"update",
"(",
"self",
")",
":",
"self",
".",
"_controller",
".",
"update",
"(",
"self",
".",
"_id",
",",
"wake_if_asleep",
"=",
"False",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"get_climate_params",
"(",
"self",
".",
"_id",
")",
"if"... | Update the temperature. | [
"Update",
"the",
"temperature",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/climate.py#L181-L189 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | ChargerSwitch.update | def update(self):
"""Update the charging state of the Tesla Vehicle."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_charging_params(self._id)
if data and (time.time() - self.__manual_update_time > 60):
if data['charging_state'] != "Char... | python | def update(self):
"""Update the charging state of the Tesla Vehicle."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_charging_params(self._id)
if data and (time.time() - self.__manual_update_time > 60):
if data['charging_state'] != "Char... | [
"def",
"update",
"(",
"self",
")",
":",
"self",
".",
"_controller",
".",
"update",
"(",
"self",
".",
"_id",
",",
"wake_if_asleep",
"=",
"False",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"get_charging_params",
"(",
"self",
".",
"_id",
")",
"if... | Update the charging state of the Tesla Vehicle. | [
"Update",
"the",
"charging",
"state",
"of",
"the",
"Tesla",
"Vehicle",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L44-L52 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | ChargerSwitch.start_charge | def start_charge(self):
"""Start charging the Tesla Vehicle."""
if not self.__charger_state:
data = self._controller.command(self._id, 'charge_start',
wake_if_asleep=True)
if data and data['response']['result']:
self.__c... | python | def start_charge(self):
"""Start charging the Tesla Vehicle."""
if not self.__charger_state:
data = self._controller.command(self._id, 'charge_start',
wake_if_asleep=True)
if data and data['response']['result']:
self.__c... | [
"def",
"start_charge",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"__charger_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'charge_start'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data"... | Start charging the Tesla Vehicle. | [
"Start",
"charging",
"the",
"Tesla",
"Vehicle",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L54-L61 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | ChargerSwitch.stop_charge | def stop_charge(self):
"""Stop charging the Tesla Vehicle."""
if self.__charger_state:
data = self._controller.command(self._id, 'charge_stop',
wake_if_asleep=True)
if data and data['response']['result']:
self.__charger_... | python | def stop_charge(self):
"""Stop charging the Tesla Vehicle."""
if self.__charger_state:
data = self._controller.command(self._id, 'charge_stop',
wake_if_asleep=True)
if data and data['response']['result']:
self.__charger_... | [
"def",
"stop_charge",
"(",
"self",
")",
":",
"if",
"self",
".",
"__charger_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'charge_stop'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data",
"and",
... | Stop charging the Tesla Vehicle. | [
"Stop",
"charging",
"the",
"Tesla",
"Vehicle",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L63-L70 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | RangeSwitch.update | def update(self):
"""Update the status of the range setting."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_charging_params(self._id)
if data and (time.time() - self.__manual_update_time > 60):
self.__maxrange_state = data['charge_to_ma... | python | def update(self):
"""Update the status of the range setting."""
self._controller.update(self._id, wake_if_asleep=False)
data = self._controller.get_charging_params(self._id)
if data and (time.time() - self.__manual_update_time > 60):
self.__maxrange_state = data['charge_to_ma... | [
"def",
"update",
"(",
"self",
")",
":",
"self",
".",
"_controller",
".",
"update",
"(",
"self",
".",
"_id",
",",
"wake_if_asleep",
"=",
"False",
")",
"data",
"=",
"self",
".",
"_controller",
".",
"get_charging_params",
"(",
"self",
".",
"_id",
")",
"if... | Update the status of the range setting. | [
"Update",
"the",
"status",
"of",
"the",
"range",
"setting",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L97-L102 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | RangeSwitch.set_max | def set_max(self):
"""Set the charger to max range for trips."""
if not self.__maxrange_state:
data = self._controller.command(self._id, 'charge_max_range',
wake_if_asleep=True)
if data['response']['result']:
self.__maxr... | python | def set_max(self):
"""Set the charger to max range for trips."""
if not self.__maxrange_state:
data = self._controller.command(self._id, 'charge_max_range',
wake_if_asleep=True)
if data['response']['result']:
self.__maxr... | [
"def",
"set_max",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"__maxrange_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'charge_max_range'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data"... | Set the charger to max range for trips. | [
"Set",
"the",
"charger",
"to",
"max",
"range",
"for",
"trips",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L104-L111 | train |
zabuldon/teslajsonpy | teslajsonpy/charger.py | RangeSwitch.set_standard | def set_standard(self):
"""Set the charger to standard range for daily commute."""
if self.__maxrange_state:
data = self._controller.command(self._id, 'charge_standard',
wake_if_asleep=True)
if data and data['response']['result']:
... | python | def set_standard(self):
"""Set the charger to standard range for daily commute."""
if self.__maxrange_state:
data = self._controller.command(self._id, 'charge_standard',
wake_if_asleep=True)
if data and data['response']['result']:
... | [
"def",
"set_standard",
"(",
"self",
")",
":",
"if",
"self",
".",
"__maxrange_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'charge_standard'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data",
"... | Set the charger to standard range for daily commute. | [
"Set",
"the",
"charger",
"to",
"standard",
"range",
"for",
"daily",
"commute",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/charger.py#L113-L120 | train |
zabuldon/teslajsonpy | teslajsonpy/lock.py | Lock.unlock | def unlock(self):
"""Unlock the doors and extend handles where applicable."""
if self.__lock_state:
data = self._controller.command(self._id, 'door_unlock',
wake_if_asleep=True)
if data['response']['result']:
self.__lock... | python | def unlock(self):
"""Unlock the doors and extend handles where applicable."""
if self.__lock_state:
data = self._controller.command(self._id, 'door_unlock',
wake_if_asleep=True)
if data['response']['result']:
self.__lock... | [
"def",
"unlock",
"(",
"self",
")",
":",
"if",
"self",
".",
"__lock_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'door_unlock'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data",
"[",
"'respon... | Unlock the doors and extend handles where applicable. | [
"Unlock",
"the",
"doors",
"and",
"extend",
"handles",
"where",
"applicable",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/lock.py#L66-L73 | train |
zabuldon/teslajsonpy | teslajsonpy/lock.py | ChargerLock.lock | def lock(self):
"""Close the charger door."""
if not self.__lock_state:
data = self._controller.command(self._id, 'charge_port_door_close',
wake_if_asleep=True)
if data['response']['result']:
self.__lock_state = True
... | python | def lock(self):
"""Close the charger door."""
if not self.__lock_state:
data = self._controller.command(self._id, 'charge_port_door_close',
wake_if_asleep=True)
if data['response']['result']:
self.__lock_state = True
... | [
"def",
"lock",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"__lock_state",
":",
"data",
"=",
"self",
".",
"_controller",
".",
"command",
"(",
"self",
".",
"_id",
",",
"'charge_port_door_close'",
",",
"wake_if_asleep",
"=",
"True",
")",
"if",
"data",... | Close the charger door. | [
"Close",
"the",
"charger",
"door",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/lock.py#L128-L135 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.wake_up | def wake_up(func):
# pylint: disable=no-self-argument
# issue is use of wraps on classmethods which should be replaced:
# https://hynek.me/articles/decorators/
"""Wrap a API f so it will attempt to wake the vehicle if asleep.
The command f is run once if the vehicle_id was la... | python | def wake_up(func):
# pylint: disable=no-self-argument
# issue is use of wraps on classmethods which should be replaced:
# https://hynek.me/articles/decorators/
"""Wrap a API f so it will attempt to wake the vehicle if asleep.
The command f is run once if the vehicle_id was la... | [
"def",
"wake_up",
"(",
"func",
")",
":",
"@",
"wraps",
"(",
"func",
")",
"def",
"wrapped",
"(",
"*",
"args",
",",
"**",
"kwargs",
")",
":",
"def",
"valid_result",
"(",
"result",
")",
":",
"try",
":",
"return",
"(",
"result",
"is",
"not",
"None",
... | Wrap a API f so it will attempt to wake the vehicle if asleep.
The command f is run once if the vehicle_id was last reported
online. Assuming f returns None and wake_if_asleep is True, 5 attempts
will be made to wake the vehicle to reissue the command. In addition,
if there is a `could_... | [
"Wrap",
"a",
"API",
"f",
"so",
"it",
"will",
"attempt",
"to",
"wake",
"the",
"vehicle",
"if",
"asleep",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L95-L209 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.post | def post(self, vehicle_id, command, data=None, wake_if_asleep=True):
# pylint: disable=unused-argument
"""Send post command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the own... | python | def post(self, vehicle_id, command, data=None, wake_if_asleep=True):
# pylint: disable=unused-argument
"""Send post command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the own... | [
"def",
"post",
"(",
"self",
",",
"vehicle_id",
",",
"command",
",",
"data",
"=",
"None",
",",
"wake_if_asleep",
"=",
"True",
")",
":",
"data",
"=",
"data",
"or",
"{",
"}",
"return",
"self",
".",
"__connection",
".",
"post",
"(",
"'vehicles/%i/%s'",
"%"... | Send post command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car across
differen... | [
"Send",
"post",
"command",
"to",
"the",
"vehicle_id",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L216-L245 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.get | def get(self, vehicle_id, command, wake_if_asleep=False):
# pylint: disable=unused-argument
"""Send get command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpo... | python | def get(self, vehicle_id, command, wake_if_asleep=False):
# pylint: disable=unused-argument
"""Send get command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpo... | [
"def",
"get",
"(",
"self",
",",
"vehicle_id",
",",
"command",
",",
"wake_if_asleep",
"=",
"False",
")",
":",
"return",
"self",
".",
"__connection",
".",
"get",
"(",
"'vehicles/%i/%s'",
"%",
"(",
"vehicle_id",
",",
"command",
")",
")"
] | Send get command to the vehicle_id.
This is a wrapped function by wake_up.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car across
different... | [
"Send",
"get",
"command",
"to",
"the",
"vehicle_id",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L248-L273 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.data_request | def data_request(self, vehicle_id, name, wake_if_asleep=False):
"""Get requested data from vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car a... | python | def data_request(self, vehicle_id, name, wake_if_asleep=False):
"""Get requested data from vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car a... | [
"def",
"data_request",
"(",
"self",
",",
"vehicle_id",
",",
"name",
",",
"wake_if_asleep",
"=",
"False",
")",
":",
"return",
"self",
".",
"get",
"(",
"vehicle_id",
",",
"'vehicle_data/%s'",
"%",
"name",
",",
"wake_if_asleep",
"=",
"wake_if_asleep",
")",
"[",... | Get requested data from vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car across
different endpoints.
https://tesla-api.timdor... | [
"Get",
"requested",
"data",
"from",
"vehicle_id",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L275-L300 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.command | def command(self, vehicle_id, name, data=None, wake_if_asleep=True):
"""Post name command to the vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the... | python | def command(self, vehicle_id, name, data=None, wake_if_asleep=True):
"""Post name command to the vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the... | [
"def",
"command",
"(",
"self",
",",
"vehicle_id",
",",
"name",
",",
"data",
"=",
"None",
",",
"wake_if_asleep",
"=",
"True",
")",
":",
"data",
"=",
"data",
"or",
"{",
"}",
"return",
"self",
".",
"post",
"(",
"vehicle_id",
",",
"'command/%s'",
"%",
"n... | Post name command to the vehicle_id.
Parameters
----------
vehicle_id : string
Identifier for the car on the owner-api endpoint. Confusingly it
is not the vehicle_id field for identifying the car across
different endpoints.
https://tesla-api.timdo... | [
"Post",
"name",
"command",
"to",
"the",
"vehicle_id",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L302-L328 | train |
zabuldon/teslajsonpy | teslajsonpy/controller.py | Controller.update | def update(self, car_id=None, wake_if_asleep=False, force=False):
"""Update all vehicle attributes in the cache.
This command will connect to the Tesla API and first update the list of
online vehicles assuming no attempt for at least the [update_interval].
It will then update all the ca... | python | def update(self, car_id=None, wake_if_asleep=False, force=False):
"""Update all vehicle attributes in the cache.
This command will connect to the Tesla API and first update the list of
online vehicles assuming no attempt for at least the [update_interval].
It will then update all the ca... | [
"def",
"update",
"(",
"self",
",",
"car_id",
"=",
"None",
",",
"wake_if_asleep",
"=",
"False",
",",
"force",
"=",
"False",
")",
":",
"cur_time",
"=",
"time",
".",
"time",
"(",
")",
"with",
"self",
".",
"__lock",
":",
"last_update",
"=",
"self",
".",
... | Update all vehicle attributes in the cache.
This command will connect to the Tesla API and first update the list of
online vehicles assuming no attempt for at least the [update_interval].
It will then update all the cached values for cars that are awake
assuming no update has occurred f... | [
"Update",
"all",
"vehicle",
"attributes",
"in",
"the",
"cache",
"."
] | 673ecdb5c9483160fb1b97e30e62f2c863761c39 | https://github.com/zabuldon/teslajsonpy/blob/673ecdb5c9483160fb1b97e30e62f2c863761c39/teslajsonpy/controller.py#L351-L413 | train |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.