Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the .strand
, .ref
, and .ref_db
attributes of the SeqFeature
which was done in Biopython 1.82 without a deprecation period. They are again aliases for .location.strand
etc, but now trigger deprecation warnings. See our deprecation policy. We apologize for any inconvenience, and thank you to those reporting this.
This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.8 is approaching end of life, our support for it is now deprecated.
Biopython 1.83 source releases are available from our website and PyPI, which also has pre-compiled wheels for the major platforms. We would expect the release to be on conda-forge shortly too.
Happy New Year!
]]>Our second release of 2023 is now out, albeit way later than we’d all intended.
This contains about 10 months worth of updates, so the NEWS file information is denser than usual: https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst
Also, there have been more deprecations and removals of deprecated code than typical – see the DEPRECATED file too: https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Thank you all, and also those unnamed who have helped indirectly, though bug reports or otherwise.
]]>This is the final release supporting Python version 3.6. It also supports Python versions 3.7, 3.8, and 3.9, as well as PyPy 3.6.1 v7.1.1.
The major changes in this version are listed below:
– The Seq
and MutableSeq
classes in Bio.Seq
now inherit from the same base class, ensuring their mutual consistency. In addition, both classes now store sequence data as bytes
and bytearray
objects, respectively.
– Empty or unknown sequences can now be created directly by passing None
to the Seq
class, instead of using UnknownSeq
. This latter class is now deprecated and will be removed in a future version of Biopython.
– A new module Bio.PDB.SASA
implements the Shrake-Rupley algorithm to calculate solvent accessible areas natively, without requiring third-party tools such as DSSP or NACCESS.
– Other minor improvements to the Bio.PDB
module include a new center_of_mass()
method to calculate the center of mass or center of gravity of any Entity subclass (e.g. Structure, Chain, or Residue).
– Changes in the KEGG KGML_Pathway
module now produce output files compliant with KGML v0.7.2. In addition, Bio.UniProt.GOA
now parses GPI files version 1.2.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement“, or the very similar but more commonly used “3-Clause BSD License“. See the LICENSE.rst
file for more details.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the black
tool.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
– Damien Goutte-Gattat
– Gert Hulselmans
– João Rodrigues
– Markus Piotrowski
– Sergio Valqui
– Suyash Gupta
– Vini Salazar (first contribution)
– Leighton Pritchard
The main change is that Bio.Alphabet
is no longer used. In some cases you will now have to specify expected letters, molecule type (DNA, RNA, protein), or gap character explicitly. Please consult the updated Tutorial and API documentation for guidance. This simplification has sped up many Seq
object methods. See https://biopython.org/wiki/Alphabet for more information.
Bio.SeqIO.parse()
is faster with “fastq” format due to small improvements in the Bio.SeqIO.QualityIO
module.
The SeqFeature
object’s .extract()
method can now be used for
trans-spliced locations via an optional dictionary of references.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement“, or the very similar but more commonly used “3-Clause BSD License“. See the LICENSE.rst
file for more details.
Additionally, a number of small bugs and typos have been fixed with additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and all of the tests have been reformatted with the black
tool to match the main code base.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Biopython 1.77 has been released and is available from our website and PyPI.
This is the first release since we dropped support for Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.
This release of Biopython supports Python 3.6, 3.7 and 3.8 It has also been tested on PyPy3.6.1 v7.1.1.
pairwise2
now allows the input of parameters with keywords and returns the alignments as a list of namedtuples
.
The codon tables have been updated to NCBI genetic code table version 4.5, which adds Cephalodiscidae mitochondrial as table 33.
Bio.Restriction
has been updated to the January 2020 release of REBASE.
A major contribution by Rob Miller to Bio.PDB
provides new methods to handle protein structure transformations using dihedral angles (internal coordinates). The new framework supports lossless interconversion between internal and cartesian coordinates, which, among other uses, simplifies the analysis and manipulation of coordinates of protein structures.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement“, or the very similar but more commonly used “3-Clause BSD License“. See the LICENSE.rst
file for more details.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the black
tool.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Update: And the following two whom we had initially wrongly listed under the previous release:
Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing.
This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement“, or the very similar but more commonly used “3-Clause BSD License“. See the LICENSE.rst
file for more details.
In addition to the mainstream x86_64
aka AMD64
CPU architecture, we now also test every contribution on the ARM64
, ppc64le
, and s390x
CPUs under Linux thanks to Travis CI. Further post-release testing done by Debian and other packagers and distributors of Biopython also covers these CPUs.
The Bio.motifs.PositionSpecificScoringMatrix.search()
method has been re-written: it now applies .calculate()
to chunks of the sequence to maintain a low memory footprint for long sequences.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite. There has been further work to follow the Python PEP8, PEP257 and best practice standard coding style, and more of the code style has been reformatted with the black
tool.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Biopython 1.75 has been released and is available from our website and PyPI.
This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected to work on the soon to be released Python 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0.
Note we intend to drop Python 2.7 support in early 2020.
The restriction enzyme list in Bio.Restriction has been updated to the August 2019 release of REBASE.
Bio.SeqIO
now supports reading and writing files in the native format of Christian Marck’s DNA Strider program (“xdna” format, also used by Serial Cloner), as well as reading files in the native formats of GSL Biotech’s SnapGene (“snapgene”) and Textco Biosoftware’s Gene Construction Kit (“gck”).
Bio.AlignIO
now supports GCG MSF multiple sequence alignments as the “msf” format (work funded by the National Marrow Donor Program).
The main Seq
object now has string-like .index()
and .rindex()
methods, matching the existing .find()
and .rfind()
implementations. The MutableSeq
object retains its more list-like .index()
behaviour.
The MMTFIO
class has been added that allows writing of MMTF file format files from a Biopython structure object. MMTFIO
has a similar interface to PDBIO
and MMCIFIO
, including the use of a Select
class to write out a specified selection. This final addition to read/write support for PDB/mmCIF/MMTF in Biopython allows conversion between all three file formats.
Values from mmCIF files are now read in as a list even when they consist of a single value. This change improves consistency and reduces the likelihood of making an error, but will require user code to be updated accordingly.
Bio.PDB
has been updated to support parsing REMARK 99 header entries from PDB-style Astral files.
A new keyword parameter full_sequences
was added to Bio.pairwise2
‘s pretty print method format_alignment
to restore the output of local alignments to the ‘old’ format (showing the whole sequences including the un-aligned parts instead of only showing the aligned parts).
A new function charge_at_pH(pH)
has been added to ProtParam
and IsoelectricPoint
in Bio.SeqUtils
.
The PairwiseAligner
in Bio.Align
was extended to allow generalized pairwise alignments, i.e. alignments of any Python object, for example three-letter amino acid sequences, three-nucleotide codons, and arrays of integers.
A new module substitution_matrices
was added to Bio.Align
, which includes an Array
class that can be used as a substitution matrix. As the Array
class is a subclass of a numpy array, mathematical operations can be applied to it directly, and C code that makes use of substitution matrices can directly access the numerical values stored in the substitution matrices. This module is intended as a replacement of Bio.SubsMat
, which is currently unmaintained.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”. See the LICENSE.rst
file for more details.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style. We have also started to use the black
Python code formatting tool.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Biopython 1.74 has been released and is available from our website and PyPI.
This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.
(Please note we will be dropping support for Python 2.7 in early 2020.)
Over half our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”. See the LICENSE.rst
file for more details.
Our core sequence objects (Seq
, UnknownSeq
, and MutableSeq
) now have a string-like .join()
method.
The NCBI now allows longer accessions in the GenBank file LOCUS line, meaning the fields may not always follow the historical column based positions. We no longer give a warning when parsing these. We now allow writing such files (although with a warning as support for reading them is not yet widespread).
Support for the mysqlclient
package, a fork of MySQLdb, has been added.
We now capture the IDcode field from PDB Header records.
Bio.pairwise2
‘s pretty-print output from format_alignment
has been optimized for local alignments: If they do not consist of the whole sequences, only the aligned section of the sequences are shown, together with the start positions of the sequences (in 1-based notation). Alignments of lists will now also be prettily printed.
Bio.SearchIO
now supports parsing the text output of the HHsuite protein sequence search tool. The format name is hhsuite2-text
and hhsuite3-text
, for versions 2 and 3 of HHsuite, respectively.
Bio.SearchIO
HSP objects has a new attribute called output_index
. This attribute is meant for capturing the order by which the HSP were output in the parsed file and is set with a default value of -1 for all HSP objects. It is also used for sorting the output of QueryResult.hsps
.
Bio.SeqIO.AbiIO
has been updated to preserve bytes value when parsing. The goal of this change is make the parser more robust by being able to extract string-values that are not utf-8-encoded. This affects all tag values, except for ID and description values, where they need to be extracted as strings to conform to the SeqRecord
interface. In this case, the parser will attempt to decode using utf-8
and fall back to the system encoding if that fails. This change affects Python 3 only.
Bio.motifs.mast
has been updated to parse XML output files from MAST over the plain-text output file. The goal of this change is to parse a more structured data source with minimal loss of functionality upon future MAST releases. Class structure remains the same plus an additional attribute Record.strand_handling
required for diagram parsing.
Bio.Entrez
now automatically retries HTTP requests on failure. The maximum number of tries and the sleep between them can be configured by changing Bio.Entrez.max_tries
and Bio.Entrez.sleep_between_tries
. (The defaults are 3 tries and 15 seconds, respectively.)
All tests using the older print-and-compare approach have been replaced by unit tests following Python’s standard testing framework.
On the documentation side, all the public modules, classes, methods and functions now have docstrings (built in help strings). In addition to displaying the Biopython API documentation via epydoc, we now also have the Biopython API documentation via Sphinx (which we hope to make the default in future). Furthermore, the PDF version of the Biopython Tutorial and Cookbook now uses syntax coloring for code snippets.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
For reference, checksums:
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Biopython 1.73 has been released and is available from our website and PyPI.
This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.
As in recent releases, more of our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”. See the LICENSE.rst file for more details.
The dictionary-like indexing in Bio.SeqIO
and Bio.SearchIO
will now explicitly preserve record order to match a behaviour change in the Python standard dict object. This means looping over the index will load the records in the on-disk order, which will be much faster (previously it would be effectively at random, based on the key hash sorting).
The “grant” matrix in Bio.SubsMat.MatrixInfo has been replaced as our original values taken from Gerhard Vogt’s old webpages at EMBL Heidelberg were discovered to be in error. The new values have been transformed following Vogt’s approach, taking the global maximum 215 minus the similarity scores from the original paper Grantham (1974), to give a distance measure.
Double-quote characters in GenBank feature qualifier values in Bio.SeqIO
are now escaped as per the NCBI standard. Improperly escaped values trigger a warning on parsing.
There is a new command line wrapper for the BWA-MEM sequence mapper.
The string-based FASTA parsers in
have been optimised, which also speeds up parsing FASTA files using Bio.SeqIO.FastaIO
Bio.SeqIO.parse()
.
Additionally, a number of small bugs and typos have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8, PEP257 and best practice standard coding style.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
For reference, checksums:
$ md5sum biopython-1.73* 9bab1776b3f63cb2a81715e78abfb6e0 biopython-1.73-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl a531f656ecae854adf1fc6021735c2a9 biopython-1.73-cp27-cp27m-manylinux1_i686.whl 27f5179f2493408d33e5322690f1bb7a biopython-1.73-cp27-cp27m-manylinux1_x86_64.whl 41fdb1f257cdcd030a468e7339a6c6ab biopython-1.73-cp27-cp27mu-manylinux1_i686.whl bf23d2daae5c72c2d84058bce3acd7a2 biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl d3cab98752b83cef121b7a1e8b81853c biopython-1.73-cp27-cp27m-win32.whl 178be72d7b294a2a15c92630bbee2a81 biopython-1.73-cp27-cp27m-win_amd64.whl 32fc6184cbf21faca0776251570b2c58 biopython-1.73-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 5c78b8210de0b511c208facf7325c7e6 biopython-1.73-cp34-cp34m-manylinux1_i686.whl ae414b4666900567579cc92df4223521 biopython-1.73-cp34-cp34m-manylinux1_x86_64.whl 1b0d7ba1b4c097b318213431d9b6b99e biopython-1.73-cp34-cp34m-win32.whl 04a91b6ea826596b0c8b643b743d176f biopython-1.73-cp34-cp34m-win_amd64.whl a8ecaa7bf30fd912536881228e754664 biopython-1.73-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 0676a634a73e049903a4bc36e3b60fc3 biopython-1.73-cp35-cp35m-manylinux1_i686.whl 6d4ebb6131a611a71816b0208747de55 biopython-1.73-cp35-cp35m-manylinux1_x86_64.whl 65165d6551e43bdc18e0912935f9c7fd biopython-1.73-cp35-cp35m-win32.whl 24c6352a143ea28c47bff5da754f0af9 biopython-1.73-cp35-cp35m-win_amd64.whl d11a2c7ba85a9927815fb9b6dfd9a0ac biopython-1.73-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 8898e77221359b4d4280e42a53bfbc52 biopython-1.73-cp36-cp36m-manylinux1_i686.whl fb8a38c943a9e80492ddb657e9d330a5 biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl 1f49d1a5b492639008dd674b83a8bcb7 biopython-1.73-cp36-cp36m-win32.whl f0dde83e1a7c27a107e6aeb253f29f08 biopython-1.73-cp36-cp36m-win_amd64.whl e082d026d3bb894838e389f159a8362b biopython-1.73-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 0db98f888700a7e119f39f136687c3d1 biopython-1.73-cp37-cp37m-manylinux1_i686.whl c92184fad3be8c8ba3cc3e8816603dc5 biopython-1.73-cp37-cp37m-manylinux1_x86_64.whl 58c58f52d514bd9a86df01da1db0d804 biopython-1.73-cp37-cp37m-win32.whl e32acd6a4a2c703ee5ff34cd62f83124 biopython-1.73-cp37-cp37m-win_amd64.whl d1d2e6154c2c89d6bb0e77f4a3578686 biopython-1.73.tar.gz 478d71daf63e9b57775fbd5aaa8f48f1 biopython-1.73.zip
$ sha256sum biopython-1.73* c43a47ad3397336aa7af5a0bb5ebec91aa2ae328b71421e550cf7e7f80d00f69 biopython-1.73-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 0302d5be80850fbaa93789ab516d189c9400755901cfe566a324e8fea10ed39b biopython-1.73-cp27-cp27m-manylinux1_i686.whl e5b5666724cab7983aebeb593e52dd276ff9fdabb3669d57db8b5ea303a097a5 biopython-1.73-cp27-cp27m-manylinux1_x86_64.whl 21723d79a1d15e99c823b440dd37176259dffa686e2a015919ad255d89238491 biopython-1.73-cp27-cp27mu-manylinux1_i686.whl 85d53b91406aacfef673fb3cf24873d978654fa49d52b5ab4d9c3b0d06b003d6 biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl c5beb53e2d5a5a573baaaa449a32d3adfb3d03bd7752adbcb20a62d6e8041e03 biopython-1.73-cp27-cp27m-win32.whl add575d5b81eec95381a53ca8c042e9de9e506b24734ec773690247d997eaa69 biopython-1.73-cp27-cp27m-win_amd64.whl 59610b1639a7d9c1f36a5398e748c044c21f4285230fa79fcea2cafe835f9366 biopython-1.73-cp34-cp34m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 1c4b55412c12b246b948c3bbb30e60a7b075da9770449371a731ac9987849381 biopython-1.73-cp34-cp34m-manylinux1_i686.whl aed261f47f72d63292fdf4c81197fdbc150094a34e10176647a932c83e179db9 biopython-1.73-cp34-cp34m-manylinux1_x86_64.whl 3cc401c15a85829eb6ae01babb02fbe7828548709b4dcb6d5149e94d5173ed7c biopython-1.73-cp34-cp34m-win32.whl f49558bea021cc5243e50efb38d545842153cde276e14879d6d63222065c683d biopython-1.73-cp34-cp34m-win_amd64.whl a149ea816f21ef72e1b4e6f538b13141584bdc531f864c5f1eb8b8feed71ba06 biopython-1.73-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl e7a03ae81b5507b3a668f81a58351c065fa6d8a0b77f772e183eb284c1cc4619 biopython-1.73-cp35-cp35m-manylinux1_i686.whl fce8051b05d62d7d0ff7af0999f6874bd9af17f0613e6c8664ac20c93215345a biopython-1.73-cp35-cp35m-manylinux1_x86_64.whl 99e6f78317c68b27a8b406c5595364005d43fee67f3b8ae20c3332588999442f biopython-1.73-cp35-cp35m-win32.whl 839882c1929476538f9872e7fe6617c6fbcd65989483254817effbc388feead1 biopython-1.73-cp35-cp35m-win_amd64.whl 164b9958d1714f318015900f2689fcc08859f76b11484e8f91f1f29acb4b7465 biopython-1.73-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl d120346e2eed46beaf1d0771826a18cee7c3155cc8c0dafc6ffffc74ac49e8fc biopython-1.73-cp36-cp36m-manylinux1_i686.whl 92c0940c5c2a76b559538a4eb1fc0277d3e960209c537d5b74632fa87a51a810 biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl 5542f847a860b90e742a1be8a9807aa57accacd2bccfb07b3f6511f85201af19 biopython-1.73-cp36-cp36m-win32.whl ef69ed6acf7bee26c530e40a768d060f46eef228d06aa2ea89439d3c54759bd8 biopython-1.73-cp36-cp36m-win_amd64.whl cfb44ba6cdfb1dbfc05b7e46f26286b37d35b2bb847868c9088e9b67060fd7be biopython-1.73-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl ede4e4335828a780dc2096fd0443c45efb3f8fcac741e544454997b978ad3cf3 biopython-1.73-cp37-cp37m-manylinux1_i686.whl 26f8ae8ddf06c85dab12f5aaff538593c7cec69102bb4ad968b3eb40a0477bf8 biopython-1.73-cp37-cp37m-manylinux1_x86_64.whl 93d79520586b48a2a77bec3a0623871b656c45dbb83c9b6834540f0a7232478e biopython-1.73-cp37-cp37m-win32.whl 0fa9346c8ec144da12a556861090cfe5fbb6ecd89418d6358047b90def48e032 biopython-1.73-cp37-cp37m-win_amd64.whl 70c5cc27dc61c23d18bb33b6d38d70edc4b926033aea3b7434737c731c94a5e0 biopython-1.73.tar.gz ade6ebfd01d58e7937a53f16e2d87e17509ec8335fe2573f39bdb7495e7e3d2b biopython-1.73.zip]]>
I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI:
https://biopython.org/wiki/
https://pypi.python.org/pypi/
This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0.
Internal changes to Bio.SeqIO have sped up the SeqRecord .format method and SeqIO.write (especially when used in a for loop).
The MAF alignment indexing in Bio.AlignIO.MafIO has been updated to use inclusive end co-ordinates to better handle searches at end points. This will require you to rebuild any existing MAF index files.
In this release more of our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”. See the LICENSE.rst file for more details.
The Entrez module now supports the NCBI API key. Also you can now set a custom directory for DTD and XSD files. This allows Entrez to be used in environments like AWS Lambda, which restricts write access to specific directories. Improved support for parsing NCBI Entrez XML files that use XSD schemas.
Internal changes to our C code mean that NumPy is no longer required at compile time – only at run time (and only for those modules which use NumPy).
Seq, UnknownSeq, MutableSeq and derived classes now support integer multiplication methods, matching native Python string methods.
A translate method has been added to Bio.SeqFeature that will extract a feature and translate it using the codon_start and transl_table qualifiers of the feature if they are present.
Bio.SearchIO is no longer considered experimental, and so it does not raise warnings anymore when imported.
A new pairwise sequence aligner is available in Bio.Align, as an alternative to the existing pairwise sequence aligner in Bio.pairwise2.
Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:
Thank you all.
Peter
P.S. You can follow @Biopython on Twitter
—
Checksums for interest/public record:
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$ md5sum biopython-1.72* 661d50514eaa8151192b2127f52a8f]]>5e biopython-1.72-cp27-cp27m- macosx_10_6_intel.macosx_10_9_ intel.macosx_10_9_x86_64. macosx_10_10_intel.macosx_10_ 10_x86_64.whl a66e12a83c44ee50f01888129658eb a0 biopython-1.72-cp27-cp27m- manylinux1_i686.whl d7eb8003d855b3b425e2d7b5062d39 0a biopython-1.72-cp27-cp27m- manylinux1_x86_64.whl 13b4e63a2a4c97e3fefa5360425f51 99 biopython-1.72-cp27-cp27mu- manylinux1_i686.whl a5a418d1c4b6a2e58ccb73bafdc60a 3e biopython-1.72-cp27-cp27mu- manylinux1_x86_64.whl e6ca44a18b5fc65e7ca4267f877fd9 cc biopython-1.72-cp27-cp27m- win32.whl 4978d56508b002591e7b6c931c5d54 f4 biopython-1.72-cp27-cp27m-win_ amd64.whl eed950f7b23a3c42682f3f635a135e 57 biopython-1.72-cp34-cp34m- macosx_10_6_intel.macosx_10_9_ intel.macosx_10_9_x86_64. macosx_10_10_intel.macosx_10_ 10_x86_64.whl 50e8fc0e63ca3ad524ea8c5d237ed6 b1 biopython-1.72-cp34-cp34m- manylinux1_i686.whl d20e9cfa98ee8991b7008f64a44f61 30 biopython-1.72-cp34-cp34m- manylinux1_x86_64.whl 1ea11554a42996491c847ae0cf36de 97 biopython-1.72-cp34-cp34m- win32.whl 848d5d53c3a6c60d9e94528e6cc350 87 biopython-1.72-cp34-cp34m-win_ amd64.whl bde20eb5d6abdaa6479113dc966906 03 biopython-1.72-cp35-cp35m- macosx_10_6_intel.macosx_10_9_ intel.macosx_10_9_x86_64. macosx_10_10_intel.macosx_10_ 10_x86_64.whl 75b83b673997dbae8a8fe1a6fa15d3 e3 biopython-1.72-cp35-cp35m- manylinux1_i686.whl b883f5439353885224789b9e251076 61 biopython-1.72-cp35-cp35m- manylinux1_x86_64.whl d76442d3fc18de8953936a6c5ef5a7 9f biopython-1.72-cp35-cp35m- win32.whl f043fa59e3fbd5d505599474aaed74 b5 biopython-1.72-cp35-cp35m-win_ amd64.whl dab6b61605938b75eef18fa9cae944 da biopython-1.72-cp36-cp36m- macosx_10_6_intel.macosx_10_9_ intel.macosx_10_9_x86_64. macosx_10_10_intel.macosx_10_ 10_x86_64.whl 49fd975593798f0d7a293ebe327f80 0e biopython-1.72-cp36-cp36m- manylinux1_i686.whl 8259fbf571b15dc05f0405b5e99394 ce biopython-1.72-cp36-cp36m- manylinux1_x86_64.whl 4e0d4de83b89d632a5dad9ee417306 f2 biopython-1.72-cp36-cp36m- win32.whl acdf4e57da4fc90bf7c52c76c2bf41 82 biopython-1.72-cp36-cp36m-win_ amd64.whl 418fecc41f75353fde30de73586900 ac biopython-1.72.tar.gz e1db4737caf6bd2f7443f7e3c986eb bb biopython-1.72.zip