prompt large_stringlengths 72 9.34k | completion large_stringlengths 0 7.61k |
|---|---|
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | with open(fn) as fp:
for record in SeqIO.parse(fp, 'fasta'):
yield record |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | dmod = get_decoy_mod_string(record.id)
test_name = record.id
if dmod is not None:
test_name = record.id.replace(dmod, '')
if test_name.split('|')[0] in ['sp', 'tr']:
return 'swiss'
elif test_name[:3] == 'ENS':
return 'ensembl'
else:
return False |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | mods = ['tryp_reverse', 'reverse', 'decoy', 'random', 'shuffle']
for mod in mods:
if mod in protein:
if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.start... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | if rectype == 'ensembl':
desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return record.description.split(fastadelim)[genefield] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | """Called by protein FDR module for both ENSG and e.g. Uniprot"""
for rec in parse_fasta(fastafn):
rtype = get_record_type(rec)
if rtype == 'ensembl' and outputtype == 'ensg':
yield get_ensg(rec)
elif outputtype == 'genename':
yield get_symbol(rec, rtype, fastadel... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | fields = [x.split(':') for x in record.description.split()]
try:
return [x[1] for x in fields if x[0] == 'gene' and len(x) == 2][0]
except IndexError:
raise RuntimeError('ENSEMBL detected but cannot find gene ENSG in fasta') |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | if rectype == 'ensembl':
fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2]
elif rectype == 'swiss':
fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == '... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | """Returns uniprot protein existence evidence level for a fasta header.
Evidence levels are 1-5, but we return 5 - x since sorting still demands
that higher is better."""
if rtype != 'swiss':
return -1
for item in record.description.split():
item = item.split('=')
try:
... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | test_name = record.id.replace(dmod, '') |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return 'swiss' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return 'ensembl' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return False |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | if protein.endswith('_{}'.format(mod)):
return '_{}'.format(mod)
elif protein.endswith('{}'.format(mod)):
return mod
elif protein.startswith('{}_'.format(mod)):
return '{}_'.format(mod)
elif protein.startswith('{}'.format(mo... |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return '_{}'.format(mod) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return '{}_'.format(mod) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return mod |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | desc_spl = [x.split(':') for x in record.description.split()]
try:
descix = [ix for ix, x in enumerate(desc_spl) if x[0] == 'description'][0]
except IndexError:
return 'NA'
desc = ' '.join([':'.join(x) for x in desc_spl[descix:]])[12:]
return desc |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | desc = []
for part in record.description.split()[1:]:
if len(part.split('=')) > 1:
break
desc.append(part)
return ' '.join(desc) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | break |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | yield get_ensg(rec) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | yield get_symbol(rec, rtype, fastadelim, genefield) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | fields = [x.split(':') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'gene_symbol' and len(x) == 2] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | fields = [x.split('=') for x in record.description.split()]
sym = [x[1] for x in fields if x[0] == 'GN' and len(x) == 2] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return record.description.split(fastadelim)[genefield] |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return 'NA' |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return -1 |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | return 5 - int(item[1]) |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def <|fim_middle|>(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by keep... | get_proteins_for_db |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | sym_out |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | parse_fasta |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_record_type |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_decoy_mod_string |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_description |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_other_gene |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_genes_pickfdr |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_ensg |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_symbol |
<|file_name|>fasta.py<|end_file_name|><｜fim▁begin｜>from Bio import SeqIO
def get_proteins_for_db(fastafn, fastadelim, genefield):
"""Runs through fasta file and returns proteins accession nrs, sequences
and evidence levels for storage in lookup DB. Duplicate accessions in
fasta are accepted and removed by... | get_uniprot_evidence_level |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | def __init__(self, expected_attr_type=None):
self.__expected_attr_type = expected_attr_type
@property
def attr_type(self):
if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
excep... |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | self.__expected_attr_type = expected_attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | if self.__expected_attr_type:
return self.__expected_attr_type
else:
try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return self.__parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | if self.__expected_attr_type and self.__expected_attr_type != value.attr_type:
raise ValueError('Unexpected attribute type')
self.__parser = parser.as_parser(value) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | with state.open_scope(*args, **kwargs):
self.__parser._parse(state) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | self.parser = other
return self |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return RuleCall(self, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | def __init__(self, rule, *args, **kwargs):
if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs
@property
def args(self):... |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | if not isinstance(rule, Rule):
raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__))
super(RuleCall, self).__init__(rule)
self.__args = args
self.__kwargs = kwargs |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return self.__args |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return dict(self.__kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | args = [state.invoke(a) for a in self.__args]
kwargs = {k: state.invoke(v) for k, v in self.__kwargs.items()}
self.parser._parse(state, *args, **kwargs) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return self.__expected_attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | try:
inner_parser = self.__parser
except AttributeError:
raise NotImplementedError
else:
return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | return inner_parser.attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | raise ValueError('Unexpected attribute type') |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | raise TypeError('Expected rule to be type Rule, was {}'.format(type(rule).__name__)) |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | __init__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | attr_type |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | parser |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | _parse |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | __imod__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | __call__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | __init__ |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | args |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | kwargs |
<|file_name|>rule.py<|end_file_name|><｜fim▁begin｜># Copyright 2015 Rafe Kaplan
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless req... | _parse |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
<｜fim▁hole｜>
class Superhero(ModelBase):
name = models.CharField(max_length=256, editable=False)
class Meta:
verbose_name_plural = _("Su... | |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
class Superhero(ModelBase):
<|fim_middle|>
<｜fim▁end｜> | name = models.CharField(max_length=256, editable=False)
class Meta:
verbose_name_plural = _("Superheroes") |
<|file_name|>models.py<|end_file_name|><｜fim▁begin｜>from django.utils.translation import ugettext as _
from django.db import models
from jmbo.models import ModelBase
class Superhero(ModelBase):
name = models.CharField(max_length=256, editable=False)
class Meta:
<|fim_middle|>
<｜fim▁end｜> | verbose_name_plural = _("Superheroes") |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... |
.. moduleauthor:: Sebastian Wiesner <lunaryorn@gmail.com>
""" |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | """An observer for device events integrating into the :mod:`PyQt4` mainloop.
This class inherits :class:`~PyQt4.QtCore.QObject` to turn device events
into Qt signals:
>>> from pyudev import Context, Monitor
>>> from pyudev.pyqt4 import MonitorObserver
>>> context = Context()
>>> monitor = ... |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | """
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
... |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | """An observer for device events integrating into the :mod:`PyQt4` mainloop.
.. deprecated:: 0.17
Will be removed in 1.0. Use :class:`MonitorObserver` instead.
"""
#: emitted upon arbitrary device events
deviceEvent = pyqtSignal(text_type, Device)
#: emitted, if a device was added
... |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | """
Observe the given ``monitor`` (a :class:`~pyudev.Monitor`):
``parent`` is the parent :class:`~PyQt4.QtCore.QObject` of this
object. It is passed unchanged to the inherited constructor of
:class:`~PyQt4.QtCore.QObject`.
"""
QObject.__init__(self, parent)
... |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | __init__ |
<|file_name|>pyqt4.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
# Copyright (C) 2010, 2011, 2012, 2013 Sebastian Wiesner <lunaryorn@gmail.com>
# This library is free software; you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by the
# Free Softw... | __init__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | self.count = 0
tm = MyTaskManager(config, task_func=mock.Mock()) |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | def test_constuctor1(self):
config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False
def test_get_iterator(self):
config = DotDict()
... |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config)
assert tm.config == config
assert tm.task_func == default_task_func
assert tm.quit is False |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | config = DotDict()
config.quit_on_empty_queue = False
tm = TaskManager(config, job_source_iterator=range(1))
assert list(tm._get_iterator()) == [0]
def an_iter(self):
yield from range(5)
tm = TaskManager(config, job_source_iterator=an_iter)
assert l... |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | yield from range(5) |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | def __init__(self, config):
self.config = config
def __iter__(self):
yield from self.config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | self.config = config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | yield from self.config |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = False
class MyTaskManager(TaskManager):
def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise... |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | def _responsive_sleep(self, seconds, wait_log_interval=0, wait_reason=""):
try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | try:
if self.count >= 2:
raise KeyboardInterrupt
self.count += 1
except AttributeError:
self.count = 0 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | config = DotDict()
config.idle_delay = 1
config.quit_on_empty_queue = True
tm = TaskManager(config, task_func=mock.Mock())
waiting_func = mock.Mock()
tm.blocking_start(waiting_func=waiting_func)
assert tm.task_func.call_count == 10
assert waiting_func.... |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | raise KeyboardInterrupt |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | test_constuctor1 |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | test_get_iterator |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | an_iter |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | __init__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | __iter__ |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | test_blocking_start |
<|file_name|>test_task_manager.py<|end_file_name|><｜fim▁begin｜># This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from unittest import mock
from configman.dotdict import ... | _responsive_sleep |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.