repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
biopython | Bio/AlignIO/ClustalIO.py | .py | # Copyright 2006-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.AlignIO support ... | 314 | 12,152 |
biopython | Bio/SVDSuperimposer/__init__.py | .py | # Copyright (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Align on protein st... | 204 | 6,256 |
biopython | Bio/Data/CodonTable.py | .py | # Copyright 2000 Andrew Dalke. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Codon tables based on thos... | 1,309 | 50,509 |
biopython | Bio/Data/PDBData.py | .py | # Copyright 2022 Joao Rodrigues. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Alphabets used by the ww... | 389 | 22,894 |
biopython | Bio/Data/IUPACData.py | .py | # Copyright 2000 Andrew Dalke. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Information about the IUPA... | 421 | 9,223 |
biopython | Bio/phenotype/pm_fitting.py | .py | # Copyright 2014-2016 by Marco Galardini. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Growth curves f... | 152 | 4,208 |
biopython | Bio/phenotype/__init__.py | .py | # Copyright 2014-2016 by Marco Galardini. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
r"""phenotype data... | 245 | 8,353 |
biopython | Bio/phenotype/phen_micro.py | .py | # Copyright 2014-2016 by Marco Galardini. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes to work... | 1,210 | 37,710 |
biopython | Bio/Blast/NCBIXML.py | .py | # Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# Copyright 2000 by Bertrand Frottier. All rights reserved.
# Revisions 2005-2006 copyright Michiel de Hoon
# Revisions 2006-2009 copyright Peter Cock
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython Licens... | 1,332 | 49,592 |
biopython | Bio/Blast/__init__.py | .py | # Copyright 1999 by Jeffrey Chang. All rights reserved.
# Revisions 2023 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been in... | 1,353 | 51,446 |
biopython | Bio/Blast/NCBIWWW.py | .py | # Copyright 1999 by Jeffrey Chang. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Patched by Brad Chapm... | 374 | 14,116 |
biopython | Bio/Blast/_writers.py | .py | import codecs
import html
from abc import ABC
from abc import abstractmethod
from Bio.Seq import UndefinedSequenceError
def _html_entity_replace(error):
start = error.start
end = error.end
character = error.object[start:end]
codepoint = ord(character)
entity = f"&{html.entities.codepoint2name... | 1,521 | 39,674 |
biopython | Bio/Blast/_parser.py | .py | # Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2000 by Bertrand Frottier. All rights reserved.
# Revisions 2005-2006 copyright Michiel de Hoon
# Revisions 2006-2009 copyright Peter Cock
# Revisions 2023 by Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution ... | 1,227 | 41,603 |
biopython | Bio/Graphics/DisplayRepresentation.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Represent information f... | 184 | 6,749 |
biopython | Bio/Graphics/KGML_vis.py | .py | # Copyright 2013 Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Classes and function... | 443 | 17,637 |
biopython | Bio/Graphics/__init__.py | .py | # Copyright 2008 by Brad Chapman. All rights reserved.
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# Copyright 2009-2017 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License... | 93 | 3,300 |
biopython | Bio/Graphics/BasicChromosome.py | .py | # Copyright 2001, 2003 by Brad Chapman. All rights reserved.
# Revisions copyright 2011 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should ha... | 820 | 31,526 |
biopython | Bio/Graphics/Comparative.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Plots to compare inform... | 182 | 6,632 |
biopython | Bio/Graphics/Distribution.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Display information dis... | 253 | 9,301 |
biopython | Bio/Graphics/ColorSpiral.py | .py | # Copyright 2012 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Generate RGB colo... | 206 | 7,349 |
biopython | Bio/Graphics/GenomeDiagram/_Track.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: ... | 285 | 11,662 |
biopython | Bio/Graphics/GenomeDiagram/_CrossLink.py | .py | # Copyright 2011-2017 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Genome Diagram Featu... | 101 | 3,309 |
biopython | Bio/Graphics/GenomeDiagram/_FeatureSet.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: ... | 208 | 7,774 |
biopython | Bio/Graphics/GenomeDiagram/__init__.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2009 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included ... | 38 | 1,172 |
biopython | Bio/Graphics/GenomeDiagram/_Diagram.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: ... | 412 | 15,633 |
biopython | Bio/Graphics/GenomeDiagram/_CircularDrawer.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2017 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been incl... | 1,732 | 68,783 |
biopython | Bio/Graphics/GenomeDiagram/_Graph.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2009 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been incl... | 191 | 6,838 |
biopython | Bio/Graphics/GenomeDiagram/_LinearDrawer.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2009 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been incl... | 1,585 | 63,449 |
biopython | Bio/Graphics/GenomeDiagram/_Feature.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: ... | 198 | 8,064 |
biopython | Bio/Graphics/GenomeDiagram/_GraphSet.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2010 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been incl... | 172 | 5,634 |
biopython | Bio/Graphics/GenomeDiagram/_AbstractDrawer.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2017 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been incl... | 566 | 18,539 |
biopython | Bio/Graphics/GenomeDiagram/_Colors.py | .py | # Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Contact: ... | 235 | 9,678 |
biopython | Bio/Entrez/__init__.py | .py | # Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# Copyright 2008-2013 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2011-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2015 by Eric Rasche. All rights reserved.
# Revisions copyright 2015 by Carlos Pena. All rights reserved... | 748 | 29,644 |
biopython | Bio/Entrez/Parser.py | .py | # Copyright 2008-2014 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2008-2015 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that sho... | 1,166 | 46,942 |
biopython | Bio/Geo/__init__.py | .py | # Copyright 2001 by Katharine Lindner. All rights reserved.
# Copyright 2006 by PeterC. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part... | 68 | 2,176 |
biopython | Bio/Geo/Record.py | .py | # Copyright 2001 by Katharine Lindner. All rights reserved.
# Copyright 2006 by PeterC. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Hold GEO data in a straightforward fo... | 91 | 2,972 |
biopython | Bio/Restriction/PrintFormat.py | .py | #!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
r"""Print the results of restriction enzyme... | 486 | 16,232 |
biopython | Bio/Restriction/Restriction.py | .py | #!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Restriction Enzyme classes.
Notes abou... | 2,641 | 83,768 |
biopython | Bio/NMR/NOEtools.py | .py | # Copyright 2004 by Bob Bussell. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""NOEtools: For predicting NOE coordinates from assignment data.
The input and output are model... | 101 | 3,353 |
biopython | Bio/NMR/__init__.py | .py | # This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Code for working with NMR data.
This directory currently contains contributions from:
- Bob Bussell <rgb2003@med.cornell.edu> -- NOEtools and xp... | 12 | 332 |
biopython | Bio/NMR/xpktools.py | .py | # Copyright 2004 by Bob Bussell. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tools to manipulate data from nmrview .xpk peaklist files."""
HEADERLEN = 6
class XpkEntry:... | 314 | 9,274 |
biopython | Bio/Emboss/PrimerSearch.py | .py | # Copyright 2008 Michiel de Hoon. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to interact with t... | 81 | 2,521 |
biopython | Bio/Emboss/Primer3.py | .py | # Copyright 2008 Michiel de Hoon.
# Revisions copyright 2009 Leighton Pritchard.
# Revisions copyright 2010 Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE fi... | 184 | 5,576 |
biopython | Bio/Nexus/Trees.py | .py | # Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tree... | 995 | 40,281 |
biopython | Bio/Nexus/Nexus.py | .py | # Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
# Revisions copyright 2014-2015 by Joe Cora (standard data)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that s... | 2,132 | 83,836 |
biopython | Bio/Nexus/StandardData.py | .py | # Copyright 2014 Joe Cora.
# Revisions copyright 2017 Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# pa... | 118 | 3,996 |
biopython | Bio/Nexus/Nodes.py | .py | # Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Link... | 181 | 5,828 |
biopython | Bio/UniProt/__init__.py | .py | # Copyright 2013 by Iddo Friedberg idoerg@gmail.com
# Revision copyright 2013 by Peter Cock. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been inclu... | 157 | 5,376 |
biopython | Bio/UniProt/GOA.py | .py | #!/usr/bin/env python
# Copyright 2013, 2016 by Iddo Friedberg idoerg@gmail.com. All rights reserved.
# Copyright 2020 by Sergio Valqui. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see... | 510 | 15,791 |
biopython | Bio/SeqIO/InsdcIO.py | .py | # Copyright 2007-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support fo... | 1,557 | 58,571 |
biopython | Bio/SeqIO/TwoBitIO.py | .py | # Copyright 2020 by Michiel de Hoon
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for UCSC's "twoBit" (.2bi... | 264 | 11,165 |
biopython | Bio/SeqIO/SffIO.py | .py | # Copyright 2009-2020 by Peter Cock. All rights reserved.
# Based on code contributed and copyright 2009 by Jose Blanca (COMAV-UPV).
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SeqIO sup... | 1,480 | 55,441 |
biopython | Bio/SeqIO/QualityIO.py | .py | # Copyright 2009-2020 by Peter Cock. All rights reserved.
# Copyright 2020 by Michael R. Crusoe
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of t... | 2,527 | 96,018 |
biopython | Bio/SeqIO/PirIO.py | .py | # Copyright 2008-2015 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support fo... | 293 | 10,021 |
biopython | Bio/SeqIO/GfaIO.py | .py | """Bio.SeqIO support for the Graphical Fragment Assembly format.
This format is output by many assemblers and includes linkage information for
how the different sequences fit together, however, we just care about the
segment (sequence) information.
Documentation:
- Version 1.x: https://gfa-spec.github.io/GFA-spec/GFA... | 216 | 7,221 |
biopython | Bio/SeqIO/SeqXmlIO.py | .py | # Copyright 2010 by Thomas Schmitt.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for the "seqxml" file for... | 728 | 30,529 |
biopython | Bio/SeqIO/AceIO.py | .py | # Copyright 2008-2015 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support fo... | 124 | 4,830 |
biopython | Bio/SeqIO/PhdIO.py | .py | # Copyright 2008-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2009 by Cymon J. Cox. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should hav... | 171 | 6,391 |
biopython | Bio/SeqIO/XdnaIO.py | .py | # Copyright 2017-2019 Damien Goutte-Gattat. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO sup... | 366 | 12,404 |
biopython | Bio/SeqIO/__init__.py | .py | # Copyright 2006-2024 by Peter Cock. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
r"""Sequence input/output... | 1,173 | 45,803 |
biopython | Bio/SeqIO/UniprotIO.py | .py | # Copyright 2010 by Andrea Pierleoni
# Revisions copyright 2010, 2016 by Peter Cock
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as... | 572 | 24,714 |
biopython | Bio/SeqIO/SnapGeneIO.py | .py | # Copyright 2017-2019 Damien Goutte-Gattat. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO sup... | 357 | 12,451 |
biopython | Bio/SeqIO/IgIO.py | .py | # Copyright 2008-2015 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support fo... | 125 | 4,068 |
biopython | Bio/SeqIO/SwissIO.py | .py | # Copyright 2006-2013,2020 by Peter Cock.
# Revisions copyright 2008-2009 by Michiel de Hoon.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been i... | 125 | 5,327 |
biopython | Bio/SeqIO/PdbIO.py | .py | # Copyright 2012 by Eric Talevich. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support for ... | 578 | 22,951 |
biopython | Bio/SeqIO/FastaIO.py | .py | # Copyright 2006-2017,2020 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# This module is... | 687 | 22,400 |
biopython | Bio/SeqIO/NibIO.py | .py | # Copyright 2019 by Michiel de Hoon. All rights reserved.
# Based on code contributed and copyright 2016 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have be... | 176 | 5,857 |
biopython | Bio/SeqIO/AbiIO.py | .py | # Copyright 2011 by Wibowo Arindrarto (w.arindrarto@gmail.com)
# Revisions copyright 2011-2016 by Peter Cock.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included... | 606 | 26,249 |
biopython | Bio/SeqIO/GckIO.py | .py | # Copyright 2019 Damien Goutte-Gattat. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support ... | 246 | 9,055 |
biopython | Bio/SeqIO/_index.py | .py | # Copyright 2009-2011 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Dictionary like inde... | 719 | 27,642 |
biopython | Bio/SeqIO/Interfaces.py | .py | # Copyright 2006-2021 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO support mo... | 250 | 8,419 |
biopython | Bio/SeqIO/TabIO.py | .py | # Copyright 2008-2017,2020 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SeqIO suppo... | 159 | 5,196 |
biopython | Bio/Medline/__init__.py | .py | # Copyright 1999 by Jeffrey Chang. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to work with Med... | 226 | 6,272 |
biopython | Bio/SearchIO/_utils.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Common SearchIO util... | 170 | 5,596 |
biopython | Bio/SearchIO/__init__.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Biopython interface... | 685 | 29,177 |
biopython | Bio/SearchIO/BlatIO.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser ... | 756 | 31,398 |
biopython | Bio/SearchIO/FastaIO.py | .py | # Adapted from Bio.AlignIO.FastaIO copyright 2008-2011 by Peter Cock.
# Copyright 2012 by Wibowo Arindrarto.
# All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that shoul... | 603 | 25,993 |
biopython | Bio/SearchIO/_index.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# Revisions copyright 2012-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that shoul... | 36 | 1,233 |
biopython | Bio/SearchIO/HHsuiteIO/__init__.py | .py | # Copyright 2019 by Jens Thomas. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO support for ... | 18 | 639 |
biopython | Bio/SearchIO/HHsuiteIO/hhsuite2_text.py | .py | # Copyright 2019 by Jens Thomas. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser for HH... | 237 | 9,354 |
biopython | Bio/SearchIO/BlastIO/blast_tab.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO pars... | 896 | 33,824 |
biopython | Bio/SearchIO/BlastIO/__init__.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO supp... | 339 | 17,923 |
biopython | Bio/SearchIO/BlastIO/blast_xml.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO pars... | 984 | 37,031 |
biopython | Bio/SearchIO/InterproscanIO/__init__.py | .py | # Copyright 2018 by Adhemar Zerlotini. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO suppor... | 97 | 5,155 |
biopython | Bio/SearchIO/InterproscanIO/interproscan_xml.py | .py | # Copyright 2018 by Adhemar Zerlotini. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parse... | 197 | 7,547 |
biopython | Bio/SearchIO/HmmerIO/_base.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO base cl... | 46 | 1,482 |
biopython | Bio/SearchIO/HmmerIO/hmmer2_text.py | .py | # Copyright 2012 by Kai Blin. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser for HMMER... | 378 | 12,932 |
biopython | Bio/SearchIO/HmmerIO/__init__.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO support... | 308 | 20,466 |
biopython | Bio/SearchIO/HmmerIO/hmmer3_domtab.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser ... | 379 | 14,071 |
biopython | Bio/SearchIO/HmmerIO/hmmer3_text.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser ... | 458 | 20,043 |
biopython | Bio/SearchIO/HmmerIO/hmmer3_tab.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser ... | 338 | 12,910 |
biopython | Bio/SearchIO/InfernalIO/infernal_text.py | .py | # Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser f... | 543 | 21,628 |
biopython | Bio/SearchIO/InfernalIO/_base.py | .py | # Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO base cla... | 40 | 1,415 |
biopython | Bio/SearchIO/InfernalIO/__init__.py | .py | # Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO support ... | 234 | 15,555 |
biopython | Bio/SearchIO/InfernalIO/infernal_tab.py | .py | # Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO parser fo... | 487 | 14,945 |
biopython | Bio/SearchIO/_model/hit.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO object ... | 465 | 17,396 |
biopython | Bio/SearchIO/_model/_base.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Abstract base classe... | 70 | 2,671 |
biopython | Bio/SearchIO/_model/__init__.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO objects... | 60 | 2,479 |
biopython | Bio/SearchIO/_model/hsp.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO objects... | 1,226 | 48,206 |
biopython | Bio/SearchIO/_model/query.py | .py | # Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Bio.SearchIO object ... | 738 | 30,199 |
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