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#!/usr/bin/env python
"""
This script extracts nucleotide or protein sequences from a GenBank file in accordance with a list of
(locus_tag/gene, feature type) tuples.
Required modules: Python 3, BioPython, argparse, csv.
Usage:
python extractSeqFromGBK.py --targets [target file] --gbk [GenBank file(s)] > [output... | wanyuac/BINF_toolkit | extractSeqFromGBK.py | Python | gpl-3.0 | 10,257 | [
"Biopython"
] | a3357e3fe2ec99698cb78698fbdf211ee80611429f0e86ecfdf235ed6d3dc7d4 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | Forage/Gramps | gramps/plugins/tool/desbrowser.py | Python | gpl-2.0 | 5,538 | [
"Brian"
] | b8ce3557fc26357bd84c3c759bcfbc15ec96470d416f361be068438a840bf960 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGenelendatabase(RPackage):
"""Lengths of mRNA transcripts for a number of genomes.
... | iulian787/spack | var/spack/repos/builtin/packages/r-genelendatabase/package.py | Python | lgpl-2.1 | 1,123 | [
"Bioconductor"
] | 5f597510c4ebc1d0e1a06a2c398426f3bf6865349355c9d00ceaaac531e1e31f |
from __future__ import division
from __future__ import absolute_import
import tensorflow as tf
import numpy as np
from six.moves import range
from datetime import datetime
from memn2n.modules import *
def zero_nil_slot(t, name=None):
"""
Overwrites the nil_slot (first row) of the input Tensor with zeros.
... | Amber819/chatbot_AM | memn2n/attentionn2n_dialog.py | Python | mit | 15,251 | [
"Gaussian"
] | ec03119486de8d877f505dfb4b2e9393119c2d8ebdc714a9c99205e75431ecdc |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import random
import re
import unittest
import warnings
import requests
from ruamel.yaml import YAML
from pymatgen.analysis.phase_diagram import PhaseDiagram
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, Pou... | materialsproject/pymatgen | pymatgen/ext/tests/test_matproj.py | Python | mit | 22,788 | [
"pymatgen"
] | 945b8f420825c9e2d46496b6265d8335de940d1607306baa2b4f4ea98245f940 |
#! /usr/bin/env python
# coding=utf8
# ECDSA_256k1 of FastSignVerify
# Copyright (C) 2014 Antoine FERRON
# Some portions based on :
# "python-ecdsa" Copyright (C) 2010 Brian Warner (MIT Licence)
# "Simple Python elliptic curves and ECDSA" Copyright (C) 2005 Peter Pearson (public domain)
# This program is free softw... | antonio-fr/AddressGen_BTChip | ECDSA_256k1.py | Python | gpl-3.0 | 4,806 | [
"Brian"
] | 19e115dba853120253fffd95275f0a3e9d11839f7f0e6e28d7c7e3cea11e2a35 |
from __future__ import (absolute_import, division,
print_function, unicode_literals)
__all__ = ['save_to_regions', 'save_galaxy_to_regions', 'save_to_dsim']
from itertools import cycle
import numpy as np
from astropy.coordinates import SkyCoord
from astropy import units as u
from .utils impor... | adwasser/masktools | masktools/superskims/outputs.py | Python | mit | 4,094 | [
"Galaxy"
] | 8e3356dce9530b648bd9b503cde6c6d03a7d1638fa9db084fd86fc54d4ea824f |
from __future__ import division
from __future__ import unicode_literals
# Copyright 2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foun... | bastibl/gnuradio | gr-filter/python/filter/design/fir_design.py | Python | gpl-3.0 | 16,523 | [
"Gaussian"
] | 43ed90041156c3494fcce1eaf384001e09b8b5535ffab6408b4acb5b92c6b408 |
import pytest
from capybara.exceptions import ElementNotFound
from capybara.tests.helpers import extract_results
class TestSelect:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/form")
def test_returns_the_value_of_the_first_option(self, session):
assert ... | elliterate/capybara.py | capybara/tests/session/test_select.py | Python | mit | 6,109 | [
"VisIt"
] | 2dc355f330df2fef43a77b9a470863cd53d44363aff1aac0fef6e341590094c3 |
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful, but ... | h2oloopan/easymerge | EasyMerge/clonedigger/logilab/astng/utils.py | Python | mit | 6,441 | [
"VisIt"
] | f0e067eef37447878a41bb3d823e36d4823cf0f27c36c065ce14c5e31de8e28d |
import os
import numpy as nm
try:
from enthought.tvtk.api import tvtk
from enthought.mayavi.sources.vtk_data_source import VTKDataSource
from enthought.pyface.timer.api import Timer
except:
from tvtk.api import tvtk
from mayavi.sources.vtk_data_source import VTKDataSource
from pyface.timer.ap... | RexFuzzle/sfepy | sfepy/postprocess/sources.py | Python | bsd-3-clause | 12,806 | [
"Mayavi",
"VTK"
] | ab7813d408f1aec354353f4b2c4a2430cb6d853717da939ba7e346788bf7d45d |
# -*- coding: utf-8 -*-
"""Calculate PBE0 bandgaps.
The numbers are compared to:
Hybrid functionals within the all-electron FLAPW method:
implementation and applications of PBE0
Markus Betzinger, Christoph Friedrich, Stefan Blügel
Physical Review B 81, 195117 (2010)
DOI: 10.1103/PhysRevB.81.195117
"""
im... | robwarm/gpaw-symm | gpaw/test/big/pbe0/gaps.py | Python | gpl-3.0 | 2,964 | [
"ASE",
"GPAW"
] | 7fad47d3c47af008946f4ba4467bbb3d80af6a0868c610ba8403bf7c9be09ee7 |
# 411. Minimum Unique Word Abbreviation Add to List
# DescriptionHintsSubmissionsSolutions
# Total Accepted: 4460
# Total Submissions: 14034
# Difficulty: Hard
# Contributor: LeetCode
# A string such as "word" contains the following abbreviations:
#
# ["word", "1ord", "w1rd", "wo1d", "wor1", "2rd", "w2d", "wo2", "1o1d... | shawncaojob/LC | PY/411_minimum_unique_word_abbreviation.py | Python | gpl-3.0 | 1,166 | [
"Amber"
] | 890cb3482c1c3ef8b899f2baa754dcccbff0fb5682e77bbb62655d797bc7d79d |
from asposewords import Settings
from com.aspose.words import License
class ApplyLicense:
def __init__(self):
dataDir = Settings.dataDir + 'quickstart/'
# This line attempts to set a license from several locations relative to the executable and Aspose.Words.dll.
# You can also use... | aspose-words/Aspose.Words-for-Java | Plugins/Aspose_Words_Java_for_Jython/asposewords/quickstart/ApplyLicense.py | Python | mit | 911 | [
"VisIt"
] | 466bba6847fca9eeb33fd296431b4446170cf97b4fff346b97e752798a0dc421 |
"""
=================
:mod:`crossovers`
=================
.. Copyright 2012 Aaron Garrett
.. This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either ver... | hishnash/inspyred | inspyred/ec/variators/crossovers.py | Python | mit | 18,622 | [
"Gaussian"
] | 36bac07d8b1c04b4e22de73b55ce949aefd28327add987b24edf54baa9228f1e |
########################################################################
# File : ComputingElement.py
# Author : Stuart Paterson, A.T.
########################################################################
""" The Computing Element class is a base class for all the various
types CEs. It serves several purpos... | Andrew-McNab-UK/DIRAC | Resources/Computing/ComputingElement.py | Python | gpl-3.0 | 19,794 | [
"DIRAC"
] | 8897ff30c13cd4ed8395969302809ea2a778553ea3587c7f2d5d9493eb3a608f |
"""
A module to write the output in different formats
"""
import os
import gzip
from argparse import Namespace
from Bio import SeqIO
from Bio.SeqFeature import SeqFeature, FeatureLocation
from collections import OrderedDict
from BCBio import GFF # bcbio-gff package
import PhiSpyModules.version as version
from .log_... | linsalrob/PhiSpy | PhiSpyModules/writers.py | Python | mit | 15,098 | [
"Biopython"
] | 44daacbb9cebd8cea627c406b86b717841958f53a0323e9fe561fc8f18d3f08c |
"""Handling data input from sequence files in multiple formats"""
try:
from Bio import SeqIO
from Bio.Data import CodonTable
from Bio.Alphabet import IUPAC
except ImportError as e:
print('ERROR: {}'.format(e.msg))
exit(1)
def load_file(filename, file_format="fasta"):
"""
Load sequence from... | Athemis/charm | LibCharm/IO/__init__.py | Python | mit | 1,266 | [
"Biopython"
] | 3fcefedb6c73de1cea07f296cbdc94373e51fa932f61d988b3a3b0478eb30b55 |
##
# Copyright 2009-2021 Ghent University
# Copyright 2015-2021 Stanford University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum... | hpcugent/easybuild-easyblocks | easybuild/easyblocks/a/amber.py | Python | gpl-2.0 | 10,642 | [
"Amber",
"NetCDF"
] | 8a520645fb7de1ce12b97db862a95bcd85e48d1be16208db30bd83731c7196b1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# :noTabs=true:
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more inform... | zmactep/ig-folding | antibody/antibody.py | Python | bsd-3-clause | 79,267 | [
"BLAST"
] | c67f52f7fa8818290649f5628f58d571f1de0446b155a3a46d9f365fe248c041 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | appleseedhq/appleseed-maya | scripts/appleseedMaya/translator.py | Python | mit | 6,988 | [
"VisIt"
] | 600cd2e3a9992986ef53211edb5ecb1cba8a4c72159a9b59aa2b6458bb803f8f |
##
# Copyright 2012-2019 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | gppezzi/easybuild-framework | test/framework/github.py | Python | gpl-2.0 | 29,115 | [
"WIEN2k"
] | d0f3fb90c487a5d7fc6b0488472d872a3ee3273dac004b9fd97b84dd5e55b284 |
from __future__ import division
import math
import random
from collections import Sequence
from itertools import repeat
######################################
# GA Mutations #
######################################
def mutGaussian(individual, mu, sigma, indpb):
"""This function applies a g... | DailyActie/Surrogate-Model | 01-codes/deap-master/deap/tools/mutation.py | Python | mit | 8,746 | [
"Gaussian"
] | 79a2a397e1c95d2d423047bd56aa62602ecb1fb15b415bd5891a9036bbe4ac4b |
import lasagne
import lasagne.layers as L
import lasagne.nonlinearities as NL
import numpy as np
import theano
import theano.tensor as TT
from rllab.core.lasagne_layers import ParamLayer
from rllab.core.lasagne_powered import LasagnePowered
from rllab.core.network import MLP
from rllab.core.serializable import Seriali... | brain-research/mirage-rl-qprop | rllab/regressors/gaussian_mlp_regressor.py | Python | mit | 10,913 | [
"Gaussian"
] | 45f7d51850335cfa5cc2564b0c64658d8df41da53c14512b8260a541e80907ad |
#!/usr/bin/python
import subprocess, os
import SimpleHTTPServer, BaseHTTPServer, time, httplib, threading
# Local script variables
my_current_dir = "gowendotnet"
my_content_dir = "content"
my_prod_config = "gdn-prod-conf.py"
my_theme = "themes/clean-blog"
my_output = "output"
my_qa_config = "gdn-qa-conf.p... | gowenrw/gowendotnet | rwg-util.py | Python | mit | 5,369 | [
"VisIt"
] | 4f7fab4c5b972719029c818d932718919cfbce68b38d88441c2ecf90ace848e6 |
"""Find abundance of hits in blast search
"""
import pandas as pd
import os
import sys
import argparse
import re
viral_pc_df = pd.read_table('viral_ion_illumina_pc_cluster_raw_abundance.txt', header=0, index_col=0, na_values='0')
microbial_pc_df = pd.read_table('microbial_pc_cluster_raw_abundance.txt', header=0, ind... | chrisLanderson/rumen_virome | scripts/calc_core_pc.py | Python | mit | 7,503 | [
"BLAST"
] | b257414cd689222e7237905fc1a0b52635f201754dfd8fae17aea6d0c7c3c022 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
import os
import sy... | blondegeek/pymatgen | pymatgen/io/abinit/flows.py | Python | mit | 117,241 | [
"ABINIT",
"pymatgen"
] | a6091ab7956cad39379fd72c4305a65f5f863015d3596382d4ad0f65a059ddf8 |
from django.test import TestCase
from django.test.client import Client
from domain.models import Domain
from django.contrib.auth.models import User
from hq.tests.util import create_user_and_domain
from receiver.tests.util import *
class ViewsTestCase(TestCase):
def setUp(self):
create_user_a... | commtrack/temp-aquatest | apps/receiver/tests/views.py | Python | bsd-3-clause | 2,868 | [
"Brian"
] | 85488442ea791bdda4015c37ca1d3acfc2552e6e2e0c48acae7d02a7834ab16b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | rahul003/mxnet | python/mxnet/contrib/onnx/onnx2mx/_op_translations.py | Python | apache-2.0 | 26,659 | [
"Gaussian"
] | e3bfb4c5c75be9cb8b208f2680201758a78a894baaaaddfbd80199ca8e4a0991 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/tools/pathintegral.py | Python | gpl-3.0 | 9,620 | [
"ESPResSo",
"Gromacs"
] | fe228ccb9d1dfa50b0be66d9f6a80cc1bb4b5e7d928febfa9c53018ca6ef5aa2 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# 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
#
# U... | gkc1000/pyscf | pyscf/pbc/dft/numint.py | Python | apache-2.0 | 51,871 | [
"CRYSTAL",
"PySCF"
] | ae4669a49fcd0c5a125599d6879a1cacd0a5adae007a8802a20068ac5d1e1df2 |
# encoding: utf-8
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it a... | SNoiraud/gramps | gramps/plugins/tool/testcasegenerator.py | Python | gpl-2.0 | 94,161 | [
"Brian"
] | fc965d307c9c32742c6d0bf6a1a613793c902f6b5887b137d558e947c3f633af |
# -*- coding: utf-8 -*-
import numpy as np
from numpy.core.numeric import isscalar
import copy
__author__ = "amarszalek"
class Branch(object):
def __init__(self, fvalue_y):
super(Branch, self).__init__()
if len(fvalue_y) == 0:
raise ValueError('fvalue_y is empty')
self.dim = ... | amarszalek/PyOrderedFuzzyTools | pyorderedfuzzy/ofnumbers/branch.py | Python | mit | 11,276 | [
"Gaussian"
] | 4dac549d615eec8bee47d62d21fbe786483eee32c7d7ced547367c182c0b18fa |
"""
MkMov v0.4
This is a python package for making movies. It has three things it can do:
[T1] movie of a netCDF file plotting contourf output (see "python mkmov.py 2d -h");
[T2] movie of a netCDF file plotting slices of a 3d variable as a 3d cube (see "python mkmov.py 3dcube -h");
[T3] movie of a netCDF fi... | chrisb13/mkmov | examples/3dtry/greet.py | Python | gpl-3.0 | 8,145 | [
"NetCDF"
] | 893b51c39df0c0fcbb9ad73379b37625e24713f6d4eca3ea26547e8ffb4ad685 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
... | matthewalbani/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 96,380 | [
"Gaussian"
] | 378f9e61efa21ed60077ea27c7b46740c60a7cf41baf2473e1d76d07c8c0bb52 |
"""An implementation of the Zephyr Abstract Syntax Definition Language.
See http://asdl.sourceforge.net/ and
http://www.cs.princeton.edu/research/techreps/TR-554-97
Only supports top level module decl, not view. I'm guessing that view
is intended to support the browser and I'm not interested in the
browser.
... | Orav/kbengine | kbe/src/lib/python/Parser/asdl.py | Python | lgpl-3.0 | 12,192 | [
"VisIt"
] | 46fed76327e62972adc2bcf22446604dd8c0f0133776584f12761c2630e490ad |
from __future__ import print_function
import sys
import warnings
from functools import wraps
from inspect import isclass
if sys.version_info > (3,):
basestring = str
numpydoc_deprecation = """
.. deprecated:: {deprecated_in}
{problem} {remedy}
"""
class Deprecation(object):
"""
Parameters
-----... | dwhswenson/openpathsampling | openpathsampling/deprecations.py | Python | mit | 9,738 | [
"OpenMM"
] | d43f29dda8af134da83ada4d49064fdd11f1b5ba20b26cd331a15f3287bca8f7 |
#!/usr/bin/env python
import os
import sys
import unittest
import pysam
import sam_utils
class TestMISO(unittest.TestCase):
"""
Test MISO functionality.
"""
def setUp(self):
# Find out the current directory
self.miso_path = \
os.path.dirname(os.path.abspath(os.path.expandus... | nsalomonis/AltAnalyze | misopy/test_miso.py | Python | apache-2.0 | 9,027 | [
"pysam"
] | 56fec3b44d3f9a87b017eb90d54b4a45899c04eee57564aaed9604635e8322e8 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# 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
#
# U... | gkc1000/pyscf | pyscf/prop/ssc/rhf.py | Python | apache-2.0 | 17,602 | [
"Gaussian",
"PySCF"
] | c815397153488e02f755cb2a84ede8b402e534aaea8c0a30528267f562f2da0e |
from octopus.core import app
def initialise():
# if we are not to initialise the db, stop here
if not app.config.get("INITIALISE_DATABASE", False):
return
# The database and a suitable user must have been created by this point
# and a DB connection string including the db, user and pass must b... | CottageLabs/finance | service/initialise.py | Python | apache-2.0 | 1,248 | [
"Octopus"
] | e3d9fd12a8d16385024ae8335599ab723ad1e5f9acabd647632e5dc3fcfef1e9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 182,315 | [
"Psi4"
] | e5b41f120fdc19048c9efed4a11a5ffaa3e0afcb2d3ebeea43875b4d637f92d0 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source
##
## This program 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 Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/importers/branchimporter.py | Python | gpl-2.0 | 2,946 | [
"VisIt"
] | 4342e420bb89833dfbb3561a8591472373c68eafa481d6c1241987a8342f0377 |
#!/usr/bin/env python2
from . import helpers
class Neuron:
def __init__(self, weights=[], inputs=[]):
self.weights = weights
self.inputs = inputs
self.value = None
self.bias = -1
def GetValue(self, values = []):
"""
When setting Neuron.value it would be w... | jpypi/ffnn | neuron.py | Python | mit | 1,843 | [
"NEURON"
] | dba03c1753a9ed25954e42294bd25c46783fe426917cf26dabd777a1e5845006 |
#!/usr/bin/env python
def savePandas(filename, data):
"""
Save DataFrame or Series.
:param filename : Filename to use
:type filename : str
:param data: Pandas DataFrame or Series
:type data: pandas.DataFrame or pandas.Series
"""
import numpy as np
import cPickle as pickle
np.... | afrendeiro/genomeToolkit | genomeToolkit/tools.py | Python | gpl-2.0 | 47,225 | [
"Bioconductor",
"HTSeq"
] | 2114c89f70ad5dddc041dfc2958ea47fc1e6d9025b8299443780d189bf99e05c |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | vathpela/anaconda | tests/nosetests/pyanaconda_tests/pwpolicy_test.py | Python | gpl-2.0 | 1,952 | [
"Brian"
] | 2b73cf2e9a94edf078d5b0024559b8e927b8f6b0afb97f06baab29a14b6b759c |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Run through NCBI vecscreen on a local machine.
"""
import os.path as op
import sys
from jcvi.utils.range import range_merge
from jcvi.formats.fasta import tidy
from jcvi.formats.blast import BlastLine
from jcvi.formats.base import must_open
from jcvi.apps.align import... | tanghaibao/jcvi | jcvi/apps/vecscreen.py | Python | bsd-2-clause | 3,661 | [
"BLAST"
] | 44636c9dfe5f031e8ee499680f221fc7508dd93b7d657d5d61a2e1a5cf749149 |
# Grammar-Guided Feature Extraction (GGFE)
#
# Author: Damian Eads
#
# File: image_features.py
#
# Purpose: This module contains image processing primitives and
# a grammar for generating image processing programs for
# feature extraction.
#
# Date: August 8, 2009
import numpy as np
impo... | deads/ggfe | ggfe/image_features.py | Python | gpl-2.0 | 13,832 | [
"Gaussian"
] | 0540cbd65a70613153b9e3d48797fad25acf57d013b8b831f59a5a1d30400fa2 |
#! /usr/bin/env python
#
# Copyright (C) 2011, 2012, 2014, 2015 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM is free software; you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation; either version 3 o... | talbrecht/pism_pik07 | examples/inverse/tauc2tillphi.py | Python | gpl-3.0 | 10,523 | [
"NetCDF"
] | 7b21f02165e51e049a3911652279f1774d7ee56ebab7ebd280a1b62da392e0b8 |
import lb_loader
import sklearn.grid_search
import scipy.stats.distributions
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
collision_rate = 1.0 / u.picoseconds
n_steps = 500
temperat... | kyleabeauchamp/HMCNotes | code/optimize/old/test_grid.py | Python | gpl-2.0 | 1,662 | [
"OpenMM"
] | ff04cd527eaae1d9c40187b130aa188a626c402f45fbce568af3b1e430370732 |
"""Service interface is the service which provide config for client and synchronize Master/Slave servers"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import time
import re
import zipfile
import zlib
import DIRAC
from DIR... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/private/ServiceInterfaceBase.py | Python | gpl-3.0 | 14,610 | [
"DIRAC"
] | 3fa4fe2b3e03b6ed31ea2cac68866215043ce0c0d122d9e5dab851d1509c7a5d |
# ======================================================================
import localgroup
import numpy as np
# ======================================================================
class Observations(object):
"""
NAME
Observations
PURPOSE
Encode all the observational information we ha... | drphilmarshall/LocalGroupHaloProps | localgroup/observations.py | Python | gpl-2.0 | 5,309 | [
"Gaussian"
] | ee6cd186cdc1aeaff4bdc2ee501c4059409c76343bd159c69a200774debc57ab |
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# LICENSE
#
# Copyright (C) 2010-2022 GEM Foundation, G. Weatherill, M. Pagani,
# D. Monelli.
#
# The Hazard Modeller's Toolkit is free software: you can redistribute
# it and/or modify it under the terms of the GNU Affero General Public
# License a... | gem/oq-engine | openquake/hmtk/faults/mfd/characteristic.py | Python | agpl-3.0 | 7,465 | [
"Gaussian"
] | ec6a40655a6e50d1b658d6b9498719d94d877288ba7b2ec16cba11d420db9833 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | samples/lb_profile.py | Python | gpl-3.0 | 2,856 | [
"ESPResSo"
] | def5ba5d9f8c1ec8efadeede86a5eab2f5e88379f51e65e8b3f745e4a07c20ab |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 1000
n = 2000
k = 1500
testMe... | sg0/Elemental | examples/interface/QPAffineDense.py | Python | bsd-3-clause | 3,949 | [
"Gaussian"
] | b2aa276ed752283f1e6f9cee471b01111a74d659c2c0be973d2de811ae47750f |
# Copyright (c) 2005-2008, California Institute of Technology
# 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 code must retain the above copyright
# not... | strawlab/drosophila_eye_map | drosophila_eye_map/util.py | Python | bsd-2-clause | 11,451 | [
"Gaussian"
] | a7a42eb8ef6e7a4f624e4d7975457a3aecf7fe526b08212c13b5265afd0307a4 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-voms-sync
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Synchronize VOMS user data with the DIRAC Registry
"""
from __future__ import abso... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_admin_voms_sync.py | Python | gpl-3.0 | 3,210 | [
"DIRAC"
] | de9b3322c8b5cb8998744fe663d0ccbc773fff6732ad17b448961d8bbfb4cefd |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | kkreis/espressopp | src/tools/vmd.py | Python | gpl-3.0 | 5,181 | [
"ESPResSo",
"VMD"
] | 93e6c9a3c87fa8696429d3cbcedb513e2a59816f6b94cb1d4be833ffab4d999b |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
import csv
import json
import logging
import smtplib
import StringIO
from collections import namedtuple
from datetime import datetime, timedelta
from decimal import Decimal
from io import BytesIO
import pytz
from boto.... | philanthropy-u/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 91,642 | [
"VisIt"
] | be17ced9f14d2227902e01e2c933ea299e4dfb3604dd1030813cf53ad0c7f33e |
from __future__ import print_function
from typing import cast, Any, Dict, Iterable, List, Mapping, Optional, Sequence, Tuple, Text
from confirmation.models import Confirmation, create_confirmation_link
from django.conf import settings
from django.template import loader
from django.utils.timezone import now as timezon... | vaidap/zulip | zerver/lib/notifications.py | Python | apache-2.0 | 18,740 | [
"VisIt"
] | f599d1777d559b256db5439a9d5a28d263e6a7ccb459a81b109de2dc1036b29d |
from pyscf.pbc.gto import Cell
from pyscf.pbc.scf import KRKS
from pyscf.pbc.tdscf import kproxy, krhf_slow, kproxy_supercell
from test_common import assert_vectors_close
from test_krhf_slow import k2k
import unittest
from numpy import testing
import numpy
def density_fitting_ks(x):
"""
Constructs density-f... | gkc1000/pyscf | pyscf/pbc/tdscf/test/test_kproxy_ks.py | Python | apache-2.0 | 4,147 | [
"PySCF"
] | 48c8cf74b17e215a807afeec1bea32c04f4f53cefc8573aea309bbacd9d9fcfd |
from bisect import bisect_left, bisect_right
import numpy
from datetime import date, datetime
import pytz
from affine import Affine
from netCDF4 import num2date, date2num, Variable
from pyproj import Proj
import six
from trefoil.geometry.bbox import BBox
from trefoil.utilities.proj import is_latlong
from trefoil.util... | consbio/clover | trefoil/netcdf/variable.py | Python | bsd-3-clause | 20,610 | [
"NetCDF"
] | aebfa8e575ca501b7e4103116ea2c8d62b046be638dfde9e72935643f90f3383 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import re
import six
import errno
import os
import tempfile
import codecs
from monty.io import zopen
"""
This module provides utility classes for io operations.
"""
__a... | xhqu1981/pymatgen | pymatgen/util/io_utils.py | Python | mit | 6,016 | [
"pymatgen"
] | 942dd32750e818e3d495371e4d0bbfac5af02bd27ee6e4fc6b1e32a2dc5551a7 |
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# 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 required by appl... | sunqm/pyscf | pyscf/adc/test/test_radc/test_N2_radc_ip.py | Python | apache-2.0 | 3,221 | [
"PySCF"
] | a80c0fee5543ebd8e67ddd544fdfb7ed6f5e863302bcec3f9f1645df13eb2fc0 |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
MetPy Declarative Syntax Tutorial
=================================
The declarative syntax that is a part of the MetPy packaged is designed to aid in simple
data exploration and... | metpy/MetPy | v1.1/_downloads/900d76c7356d09e4ca20b90f94a0732e/declarative_tutorial.py | Python | bsd-3-clause | 21,541 | [
"NetCDF"
] | 6b19dee48423495e787f5b35388619217ef189b25713559552a6d8c0d68185d9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import simplejson as json
import decimal
import random
from collections import namedtuple
import pytest
from marshmallow import (
Schema, fields, utils, MarshalResult, UnmarshalResult,
validates, validates_schema
)
from marshmallow.exceptions import ValidationErr... | maximkulkin/marshmallow | tests/test_schema.py | Python | mit | 68,137 | [
"Brian"
] | 17c3342ccc7a49c699015a3722aab23c1b57b687e2a54acc98c227fc9af9a1b2 |
"""
awot.io.read_t28
================
Function for reading T-28 data.
See awot.io.flight.read_netcdf for a generalized version.
"""
from __future__ import absolute_import, print_function
import numpy as np
from netCDF4 import num2date
from .flight import _winduv
from . import common
def read_t28_netcdf(ncFile):
... | adlyons/AWOT | awot/io/read_t28.py | Python | gpl-2.0 | 6,545 | [
"NetCDF"
] | 2a92d0ecfbf38e870164dc4b792cd10be98ce6dc658d715da5aa62d0fea148c1 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | ericpre/hyperspy | hyperspy/signal.py | Python | gpl-3.0 | 256,881 | [
"Gaussian"
] | 475ecfe2544117a87089227f7c28d6694d70ddccd52898240ee47b3fd0f7101b |
# creates: zno.png
from ase.phasediagram import Pourbaix, solvated
refs = solvated('Zn')
print(refs)
refs += [('Zn', 0.0), ('ZnO', -3.323), ('ZnO2(aq)', -2.921)]
pb = Pourbaix(refs, Zn=1, O=1)
print(pb.decompose(1.0, 9.0))
import numpy as np
U = np.linspace(-2, 2, 200)
pH = np.linspace(-2, 16, 300)
d, names, text = pb.... | misdoro/python-ase | doc/ase/phasediagram/zno.py | Python | gpl-2.0 | 401 | [
"ASE"
] | 3cbda9e49b0369f281d007ab95b7ac4d3e1c40fea21edec82b5e5422df9eab29 |
## importing pymol
from ipymol import viewer as pymol
import os
## importing numpy and pandas
import numpy as np
import pandas as pd
# setting wd
os.chdir('/Users/alan/gdrive/documentos/doutorado/isb/20200210-ribosomeHighlighting/')
##
##RUN 'pymol -R' from main console before starting server
##
pymol.start() # St... | adelomana/30sols | SI/figure.SI7/ribosome.protein.highlighting.py | Python | gpl-3.0 | 2,205 | [
"PyMOL"
] | 062f0336b4b1d1d4362e651d29f20b5c75d8c2387ff8c34e95d32d9c27bd95f7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2019 The GraphicsFuzz Project Authors
#
# 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
#
# https://www.apache.org/licenses/LICEN... | google/graphicsfuzz | gfauto/gfauto/add_amber_tests_to_cts.py | Python | apache-2.0 | 10,616 | [
"Amber"
] | 751664c747ba68ff1fa5ef22353b64e8d6a7632a5682aa4cb2779c000f46b84d |
#
# GFSK modulation and demodulation.
#
#
# Copyright 2005,2006,2007 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | tyc85/nwsdr-3.6.3-dsc | gr-digital/python/gfsk.py | Python | gpl-3.0 | 11,318 | [
"Gaussian"
] | daf6f73ed8670d18e12d04f79a52643be5f42e8e6359f3788e559287b8e6ac5d |
import math
import numpy as np
import quaternion
import spinsfast
import spherical_functions as sf
def _process_transformation_kwargs(input_ell_max, **kwargs):
original_kwargs = kwargs.copy()
# Build the supertranslation and spacetime_translation arrays
supertranslation = np.zeros((4,), dtype=complex) #... | moble/scri | scri/asymptotic_bondi_data/transformations.py | Python | mit | 22,190 | [
"Psi4"
] | 71d629d73c45698e24297cfe39d2a07cb31df4cd522586ce456593f625e71f29 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module contains simple functions for model selection.
"""
import numpy as np
__all__ = ['bayesian_info_criterion', 'bayesian_info_criterion_lsq',
'akaike_info_criterion', 'akaike_info_criterion_lsq']
__doctest_requires__ = {'bayesia... | funbaker/astropy | astropy/stats/info_theory.py | Python | bsd-3-clause | 14,877 | [
"Gaussian"
] | 2f536f287346a69180458203b7f150bd7c7607a25aab558ce1720e4ce0d18c75 |
"""
===================================
Simple 1D Kernel Density Estimation
===================================
This example uses the :class:`~sklearn.neighbors.KernelDensity` class to
demonstrate the principles of Kernel Density Estimation in one dimension.
The first plot shows one of the problems with using histogra... | manhhomienbienthuy/scikit-learn | examples/neighbors/plot_kde_1d.py | Python | bsd-3-clause | 5,223 | [
"Gaussian"
] | 111199bb9c2d2fd7812ec6c023825450006fdccc4c851bf3103108a88f92a287 |
# encoding: utf-8
"""save.py - Window for saving one or more configurations.
"""
import gtk
from gettext import gettext as _
from copy import copy
from ase.gui.widgets import pack, cancel_apply_ok, oops, help
from ase.io import string2index, write
import numpy as np
import sys
import os
class SaveWindow(gtk.Window):
... | grhawk/ASE | tools/ase/gui/save.py | Python | gpl-2.0 | 10,260 | [
"ASE",
"CASTEP",
"FHI-aims",
"Gaussian",
"VASP"
] | a06cff969e7ec96ef59e9b1dd51a7dc4b5b6442356d1976c7c0a6ada3215af6a |
# -*- coding: utf-8 -*-
#
# RBTLIB documentation build configuration file, created by
# sphinx-quickstart on Sun May 15 17:53:16 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | bminard/rbtlib | docs/conf.py | Python | mit | 9,699 | [
"Brian"
] | 4e262cf4fbc5c649ffa9f2441b7a7b92114258cd90d0aedf93fb2756730dbbd9 |
ctca2_to_ctn = { 'AF': 'Africa',
'AN': 'Antarctica',
'AS': 'Asia',
'EU': 'Europe',
'NA': 'North America',
'OC': 'Oceania',
'SA': 'South America'}
ctn_to_ctca2 = { 'Africa': 'AF',
'Antarctica': 'AN',
'Asia': 'AS',
'Europe': 'EU',
'North America': 'NA',
'Oceania': 'OC',
... | jamesporter/InternationalTrade | countryutils/data.py | Python | mit | 48,443 | [
"BWA"
] | d7f6fa27cadacb5c661292ff2db87c1dadd56cd6c76e95ab7ef2245e59d921a5 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Applying scalar relativistic effects by decorating the scf object with
.x2c method.
Similar to the density fitting decoration, the relativistic effects can also
be applied without affecting the existed scf object.
'''
from pyscf import gto
fro... | sunqm/pyscf | examples/scf/21-x2c.py | Python | apache-2.0 | 919 | [
"PySCF"
] | d1f3a1d890dbc93b518aba2f916e3e690e63b2258a4323b8db67b8fdfd188a54 |
# -*- coding: utf-8 -*-
# Linear response with integral equations
# (c) May 2015 Aditya Gilra, EPFL.
"""
rate units evolution with Hennequin matrix
written by Aditya Gilra (c) May 2015.
"""
from brian2 import * # also does 'from pylab import *'
stand_alone = True
if stand_alone: set_device('cpp_standalone')
else: ... | adityagilra/2015_spiking_population_response | SRM_evolve.py | Python | gpl-3.0 | 7,098 | [
"NEURON"
] | 6051d375b81e58328a1ca79a58c3161ec5f8f08127aabe5cae7599acaf6ece7a |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_Me2CO_emissions_n96e_360d.py | Python | gpl-3.0 | 17,448 | [
"NetCDF"
] | dfb5ef7799682d5e45152ad0956922739f90a340ac06846bb992a67e33e567c3 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/fst/tests/test_core.py | Python | bsd-3-clause | 3,229 | [
"NEURON"
] | 3ce8420c3ec3c281e926ec7cbcd80b4c7d7f60bb0cdc456b2933d012d3e33219 |
from __future__ import unicode_literals
from functools import wraps
from os import chmod, mkdir, getuid
from os.path import dirname, exists, join
import socket
from subprocess import Popen, PIPE, call
import time
import pwd
VERSION = (0, 8, 3)
__version__ = ".".join(map(str, VERSION))
DEFAULTS = {
"box_project_... | matthiask/fh-fablib | fh_fablib/__init__.py | Python | bsd-3-clause | 8,379 | [
"GULP"
] | ee3a3aa35d1266492c7eddc8c42ba002c78cdf3f44b6d12d89221004b2dcaed5 |
"""
Testing the implemented models with cross-validation
"""
from ambiruptor.library.preprocessors.data_structures import TrainData
from ambiruptor.library.learners.models import LinearSVMClassifier
from ambiruptor.library.learners.models import RbfSVMClassifier
from ambiruptor.library.learners.models import NaiveBay... | Ambiruptor/Ambiruptor | tests/models_benchmark.py | Python | gpl-3.0 | 5,938 | [
"Gaussian"
] | 9efaa6d0fab7bbfa88dd7581cb20f2cbc861dacc50df9a01785aefcacb367a28 |
if __name__ == '__main__':
import matplotlib
matplotlib.use('Agg')
import pylab as plt
import fitsio
import astrometry.util.fits
import astrometry.util.file
import astrometry.util.plotutils
import astrometry.util.multiproc
import logging
import cytractor
import pyximport; pyximport.install(pyimport=True)... | gregreen/legacypipe | py/legacypipe/cyrunbrick.py | Python | gpl-2.0 | 1,414 | [
"Galaxy"
] | 400e3c332b52043a5601f0f723372c8388a3fb57d91fa09788d44065ced2b41c |
# mako/codegen.py
# Copyright (C) 2006-2015 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module
source code."""
#imp... | jhpyle/docassemble | docassemble_base/docassemble/base/mako/codegen.py | Python | mit | 49,608 | [
"VisIt"
] | cfcfdce625170965d881df7f457ec79dd3331cf5cf2b07379b158910787a4286 |
"""A generic client for creating and managing transformations.
See the information about transformation parameters below.
"""
from __future__ import print_function
import types
import json
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities.PromptUser import promptUser
from DIRAC.Core.Base.AP... | chaen/DIRAC | TransformationSystem/Client/Transformation.py | Python | gpl-3.0 | 26,942 | [
"DIRAC"
] | f05621e0b8738d29e2c3e4499d65682944c0a87f7ce122b8e5a804c34442b884 |
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.pyplot import Rectangle # Used to make dummy legend
# Open CSV File from Simulation
datafileS = open('../HIIregionFiles/3DHiiRegions.csv', 'r')
csvFileS = []
for row in datafileS:
csvFileS.append(row.strip().split(','))
# Save Galactic Radius Info ... | WillArmentrout/galSims | tests/completeness/Completeness_TwoPanel_O95.py | Python | gpl-2.0 | 24,461 | [
"Galaxy"
] | 9c912d482ed367bb270296e51f14aa3534d6f66ba326246b59800a53402f3c91 |
"""
This is the heart of the algorithm. Implements the objective function and mu
and sigma estimators for a Gaussian diffusion probabilistic model
"""
import numpy as np
import theano
import theano.tensor as T
from blocks.bricks import application, Initializable, Random
import regression
import util
class Diffusion... | JesseLivezey/Diffusion-Probabilistic-Models | model.py | Python | mit | 14,661 | [
"Gaussian"
] | 532589fcab95dd1375bbb6abf169fdc7a69b268e5f7c9017daa64c3272ce103b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Software License Agreement (Lesser GPL)
#
# Copyright (C) 2009-2012 Rosen Diankov <rosen.diankov@gmail.com>
#
# ikfast 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 Software... | jdsika/TUM_HOly | openrave/python/ikfast.py | Python | mit | 496,533 | [
"Gaussian"
] | 0549e6b6ddd5feb638e7f20e311e5741e6befcba4f31b15b29cbfe2172ec4130 |
SAMPLES = "sample1 sample2 sample3 sample4".split()
ROOT_FOLDER = "/path/to/root/dir"
REF_NAME = "reference_strain"
PREFIX = "snps_vs_"
REF = ROOT_DIR + "bwa_indicies/" + REF_NAME + ".fasta"
FASTQ_DIR = "fastq_files/"
RESULTS_DIR = "results/bwa/"
GENOME_DIR = ROOT_DIR + "genome_sequences/"
rule all:
input:... | jrherr/bioinformatics_scripts | manning_lab_scripts/map_reads_with_bwa_and_call_snps_with_gatk.py | Python | mit | 2,178 | [
"BWA"
] | cfa1dc5c69c52206e5d07756f21873d8302bd8172abb737572afad7da9f1c903 |
#!/usr/bin/env python
##############################################################################
#
# This PPXF_POPULATION_EXAMPLE routine shows how to study stellar population with
# the procedure PPXF, which implements the Penalized Pixel-Fitting (pPXF) method by
# Cappellari M., & Emsellem E., 2004, PASP, 116, 13... | moustakas/impy | lib/ppxf/ppxf_population_example_sdss.py | Python | gpl-2.0 | 10,172 | [
"Galaxy"
] | 95d0d2fe6847b4b452bc755535b41f868ea2688a40cf6788f68c09389da63c11 |
import datetime
from django import forms
from django.contrib.auth.models import Group
from django.forms.models import (
BaseInlineFormSet,
inlineformset_factory,
BaseModelFormSet,
modelformset_factory,
)
from cellsamples.models import Biosensor
from assays.models import (
AssayStudyConfiguration,
... | UPDDI/mps-database-server | assays/forms.py | Python | mit | 247,257 | [
"VisIt"
] | e3b478ff2ea0afeb1f6962c97c69f4bc289f17f230fef7243f285095df28a82d |
# -*- coding: utf-8 -*-
#
# MNE documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 11 10:45:48 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | cmoutard/mne-python | doc/conf.py | Python | bsd-3-clause | 9,544 | [
"Mayavi"
] | c5eb40d33d5499ab0a5ec56d3133aced29fd7ed94dccba6c2046ecdf5dcfe9fc |
from PySide import QtCore, QtGui
from geo_bsd import CovarianceModel, set_thread_num
import gui_widgets.lvmwidget as GWLvm
import gui_widgets.okwidget as GWOk
import gui_widgets.sgswidget as GWSgs
import gui_widgets.skwidget as GWSk
#from gui_widgets.cube_list import CubeItem
import hpgl_run.lvm_thread as LVMT
import h... | Snegovikufa/HPGL-GUI | gui_widgets/cont_alg_widget.py | Python | gpl-2.0 | 31,767 | [
"Gaussian"
] | dd1000bb9579fbd62b9ec98f7d68a53ff4536130f4a52bbf1dbdee37281f483d |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# 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
#
# U... | gkc1000/pyscf | pyscf/pbc/cc/__init__.py | Python | apache-2.0 | 2,078 | [
"PySCF"
] | 8870e839c2a0f0d065aa4371cba91785a9aa539a3fee7bbd812da8b253482444 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0038_auto_20150722_2116'),
]
operations = [
migrations.AddField(
model_name='staff',
... | koebbe/homeworks | visit/migrations/0039_auto_20150723_0019.py | Python | mit | 594 | [
"VisIt"
] | 825c66ff4e3f5a01e54b745d757619e36c1bbb8fe411d4419aad85ddfbc481e6 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2020 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/hole2/__init__.py | Python | gpl-2.0 | 1,658 | [
"MDAnalysis"
] | d4592075ae4fb0eedf2f4743547cab97f660eab27839c696d3620da9c7352b54 |
import collections as coll
import numpy as np
from scipy import ndimage as ndi
from ..util import img_as_float
from ..color import guess_spatial_dimensions
from .._shared.utils import warn
__all__ = ['gaussian']
def gaussian(image, sigma=1, output=None, mode='nearest', cval=0,
multichannel=None):
"... | rjeli/scikit-image | skimage/filters/_gaussian.py | Python | bsd-3-clause | 4,078 | [
"Gaussian"
] | 05a58c20f7ab7285efb93e8e941a1acf103d885db9116e6d6080f6ce8ccb26f1 |
# This file is part of Androguard.
#
# Copyright (C) 2014 Google Inc. All rights reserved.
#
# 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
... | shuxin/androguard | androguard/decompiler/dad/ast.py | Python | apache-2.0 | 24,060 | [
"VisIt"
] | aa67182cd22125b464d9e3cdc0288bdb839f4df320944bccb0b797ed98e27b46 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.AndreaConsadori.Asterisk/setup.py | Python | gpl-2.0 | 3,300 | [
"VisIt"
] | 72b0c73cf3ee90b685bad4b26146938118477477dad49a276c2cd402c518b3c0 |
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