prompt large_stringlengths 72 9.34k | completion large_stringlengths 0 7.61k |
|---|---|
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2 = args
res = op1 + op2
return (((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2 = args
res = op1 - op2
return (((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
return ExprCond(
op1 + op2 + op3.zeroExtend(op1.size),
ExprInt(0, 1),
ExprInt(1, 1),
) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
res = op1 + op2 + op3.zeroExtend(op1.size)
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (~(op1 ^ op2)))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return (((op1 ^ op2) ^ res) ^ ((op1 ^ res) & (op1 ^ op2))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
return (op1 + op2 + op3.zeroExtend(op1.size)).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
return (op1 - (op2 + op3.zeroExtend(op1.size))).msb() |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op1, op2, op3 = args
res = op1 - (op2 + op3.zeroExtend(op1.size))
return ExprCond(res, ExprInt(0, 1), ExprInt(1, 1)) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_cf, op_zf = args
return op_cf | op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_cf, = args
return ~op_cf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, op_of = args
return op_nf ^ op_of |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, op_of, op_zf = args
return ~(op_zf | (op_nf ^ op_of)) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, op_of, op_zf = args
return op_zf | (op_nf ^ op_of) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, op_of = args
return ~(op_nf ^ op_of) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_cf, op_zf = args
return ~(op_cf | op_zf) |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_cf, = args
return op_cf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, = args
return op_nf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_zf, = args
return op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_zf, = args
return ~op_zf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | op_nf, = args
return ~op_nf |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def <|fim_middle|>(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == ar... | simp_ext |
<|file_name|>simplifications_explicit.py<|end_file_name|><｜fim▁begin｜>from miasm.core.utils import size2mask
from miasm.expression.expression import ExprInt, ExprCond, ExprCompose, \
TOK_EQUAL
def simp_ext(_, expr):
if expr.op.startswith('zeroExt_'):
arg = expr.args[0]
if expr.size == arg.size... | simp_flags |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | return 0 |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | return None |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | break |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | first_time_stamp = event.timestamp |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
if event.encoder_runtime_config.HasField(decision.name):
decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['val... |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | decisions[decision.name]['time'].append(event.timestamp -
first_time_stamp)
decisions[decision.name]['value'].append(
getattr(event.encoder_runtime_config, decision.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | for metric in event.network_metrics.DESCRIPTOR.fields:
if event.network_metrics.HasField(metric.name):
metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
g... |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | metrics[metric.name]['time'].append(event.timestamp -
first_time_stamp)
metrics[metric.name]['value'].append(
getattr(event.network_metrics, metric.name)) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | print "No dump file to parse is set.\n"
parser.print_help()
exit() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | print "You have to set at least one metric or decision to plot.\n"
parser.print_help()
exit() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | f, mp_plot = plt.subplots()
plots.append(mp_plot) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | f, mp_plots = plt.subplots(plot_count, sharex=True)
plots.extend(mp_plots.tolist()) |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | main() |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | GetNextMessageSize |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | GetNextMessageFromFile |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | InitMetrics |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | InitDecisions |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | ParseAnaDump |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | main |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | data = file_to_parse.read(4)
if data == '':
return 0
return struct.unpack('<I', data)[0] |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | message_size = GetNextMessageSize(file_to_parse)
if message_size == 0:
return None
try:
event = debug_dump_pb2.Event()
event.ParseFromString(file_to_parse.read(message_size))
except IOError:
print 'Invalid message in file'
return None
return event |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | metrics = {}
event = debug_dump_pb2.Event()
for metric in event.network_metrics.DESCRIPTOR.fields:
metrics[metric.name] = {'time': [], 'value': []}
return metrics |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | decisions = {}
event = debug_dump_pb2.Event()
for decision in event.encoder_runtime_config.DESCRIPTOR.fields:
decisions[decision.name] = {'time': [], 'value': []}
return decisions |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | with open(dump_file_to_parse, 'rb') as file_to_parse:
metrics = InitMetrics()
decisions = InitDecisions()
first_time_stamp = None
while True:
event = GetNextMessageFromFile(file_to_parse)
if event == None:
break
if first_time_stamp == None:
first_time_stamp = event.ti... |
<|file_name|>parse_ana_dump.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python2
# Copyright (c) 2017 The WebRTC project authors. All Rights Reserved.
#
# Use of this source code is governed by a BSD-style license
# that can be found in the LICENSE file in the root of the source
# tree. An additional intellectual pro... | parser = OptionParser()
parser.add_option(
"-f", "--dump_file", dest="dump_file_to_parse", help="dump file to parse")
parser.add_option(
'-m',
'--metric_plot',
default=[],
type=str,
help='metric key (name of the metric) to plot',
dest='metric_keys',
action='append')... |
<|file_name|>__init__.py<|end_file_name|><｜fim▁begin｜># Copyright (c) 2021, DjaoDjin Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the abov... | # and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | new_viruses.append(v)
else:
if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | """docstring for virus_clean"""
def __init__(self,n_iqd = 5, **kwargs):
'''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd
def remove_insertions(self):
'''
remove all columns from the alignment in which the outgroup is gapped
'''
o... |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | '''
parameters
n_std -- number of interquartile distances accepted in molecular clock filter
'''
self.n_iqd = n_iqd |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | '''
remove all columns from the alignment in which the outgroup is gapped
'''
outgroup_ok = np.array(self.sequence_lookup[self.outgroup['strain']])!='-'
for seq in self.viruses:
seq.seq = Seq("".join(np.array(seq.seq)[outgroup_ok]).upper()) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | '''
remove viruses with gaps -- not part of the standard pipeline
'''
self.viruses = filter(lambda x: '-' in x.seq, self.viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | '''
substitute all ambiguous characters with '-',
ancestral inference will interpret this as missing data
'''
for v in self.viruses:
v.seq = Seq(re.sub(r'[BDEFHIJKLMNOPQRSUVWXYZ]', '-',str(v.seq))) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | '''
add a unique numerical date to each leaf. uniqueness is achieved adding a small number
'''
from date_util import numerical_date
og = self.sequence_lookup[self.outgroup['strain']]
if hasattr(og, 'date'):
try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num... |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | outgroup_date = self.sequence_lookup[self.outgroup['strain']].num_date
return np.array([x.num_date-outgroup_date for x in self.viruses if x.strain]) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | from seq_util import hamming_distance
outgroup_seq = self.sequence_lookup[self.outgroup['strain']].seq
return np.array([hamming_distance(x.seq, outgroup_seq) for x in self.viruses if x.strain]) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | """Remove viruses that don't follow a loose clock """
times = self.times_from_outgroup()
distances = self.distance_from_outgroup()
slope, intercept, r_value, p_value, std_err = stats.linregress(times, distances)
residuals = slope*times + intercept - distances
r_iqd = stats.scoreatpercentile(residuals,75) - ... |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | print "Number of viruses before cleaning:",len(self.viruses)
self.unique_date()
self.remove_insertions()
self.clean_ambiguous()
self.clean_distances()
self.viruses.sort(key=lambda x:x.num_date)
print "Number of viruses after outlier filtering:",len(self.viruses) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | try:
og.num_date = numerical_date(og.date)
except:
print "cannot parse date"
og.num_date="undefined"; |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | try:
v.num_date = numerical_date(v.date, self.date_format['fields']) + 1e-7*(ii+1)
except:
print "cannot parse date"
v.num_date="undefined"; |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | print "\tslope: " + str(slope)
print "\tr: " + str(r_value)
print "\tresiduals iqd: " + str(r_iqd) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | new_viruses.append(v) |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | if self.verbose>1:
print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | print "\t\tresidual:", r, "\nremoved ",v.strain |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | __init__ |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | remove_insertions |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | clean_gaps |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | clean_ambiguous |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | unique_date |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | times_from_outgroup |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | distance_from_outgroup |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | clean_distances |
<|file_name|>virus_clean.py<|end_file_name|><｜fim▁begin｜># clean sequences after alignment, criteria based on sequences
# make inline with canonical ordering (no extra gaps)
import os, datetime, time, re
from itertools import izip
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from scipy import sta... | clean_generic |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
pass
<｜fim▁hole｜><｜fim▁end｜> | class ContactsStaff(ContactsUser):
pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
<|fim_middle|>
class ContactsUser(SimpleContactsUser):
pass
class ContactsStaff(ContactsUser):... | pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
<|fim_middle|>
class ContactsStaff(ContactsUser):... | pass |
<|file_name|>roles.py<|end_file_name|><｜fim▁begin｜># Copyright 2015-2017 Rumma & Ko Ltd
# License: BSD (see file COPYING for details)
from lino.core.roles import UserRole
class SimpleContactsUser(UserRole):
pass
class ContactsUser(SimpleContactsUser):
pass
class ContactsStaff(ContactsUser):
<|fim_... | pass |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | """Constructeur du paramètre""" |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | ""Commande 'chemin voir'.
"""
def __init__(self):
"""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus... |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | ""Constructeur du paramètre"""
Parametre.__init__(self, "voir", "view")
self.schema = "<cle>"
self.aide_courte = "affiche le détail d'un chemin"
self.aide_longue = \
"Cette commande permet d'obtenir plus d'informations sur " \
"un chemin (ses flags actifs,... |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | Méthode appelée lors de l'ajout de la commande à l'interpréteur"""
cle = self.noeud.get_masque("cle")
cle.proprietes["regex"] = r"'[a-z0-9_:]{3,}'"
d |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | rprétation du paramètre"""
cle = dic_masques["cle"].cle
if cle not in importeur.pnj.chemins:
personnage << "|err|Ce chemin n'existe pas.|ff|"
return
chemin = importeur.pnj.chemins[cle]
msg = "Détail sur le chemin {} :".format(chemin.cle)
msg += "\... |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | e << "|err|Ce chemin n'existe pas.|ff|"
return
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | Aucune"
e |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | direction in chemin.salles.items():
msg += "\n " + salle.ident.ljust(20) + " "
msg += direction.ljust(10)
if salle in chemin.salles_retour and \
chemin.salles_retour[salle]:
msg += " (retour " + chemin.salles_ret... |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | retour " + chemin.salles_retour[salle] + ")"
|
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | _init__( |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | uter(se |
<|file_name|>voir.py<|end_file_name|><｜fim▁begin｜># -*-coding:Utf-8 -*
# Copyright (c) 2010-2017 LE GOFF Vincent
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source co... | eter(self, |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python<｜fim▁hole｜># -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = l... | |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
<|fim_middle|>
if __name__ == '__main__':
# options
startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print ... | """Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
... |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
<|fim_middle|>
def now(self):
"""Calculate current time."""
curdate = datet... | """Set birth datetime and life."""
self.birthdate = date
self.life = life
finalyear = self.birthdate.year + self.life
finaldate = datetime.datetime(finalyear, self.birthdate.month,
self.birthdate.day)
self.finaldate = finaldate - date... |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
... | """Calculate current time."""
curdate = datetime.datetime.now()
maxdays = (self.finaldate - self.birthdate).days
curdays = (curdate - self.birthdate).days
curtime = datetime.timedelta(days=1) / maxdays
curtime = curtime * curdays
return datetime.time(
... |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
... | startyear = 1900
endyear = 2000
life = 200
print startyear, "<= a <=", endyear
print "n =", life
daycount = (datetime.datetime(endyear, 12, 31) -
datetime.datetime(startyear, 1, 1)).days
birthdate = datetime.datetime(startyear, 1, 1) + \
datetime.timede... |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def __init__(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
... | year = int(args[1])
month = int(args[2])
date = int(args[3])
birthdate = datetime.datetime(year, month, date) |
<|file_name|>1-2.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# -*- coding: utf-8 -*-
import datetime
import random
import sys
class DayLife:
"""Life in a day."""
def <|fim_middle|>(self, date, life):
"""Set birth datetime and life."""
self.birthdate = date
self.life = life
... | __init__ |
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