Biopython 1.72 released
Dear Biopythoneers,
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:
- Benjamin Vaisvil (first contribution)
- Blaise Li
- Chad Parmet
- Chris Rands
- Connor T. Skennerton
- Francesco Gastaldello
- Michiel de Hoon
- Pamela Russell (first contribution)
- Peter Cock
- Spencer Bliven
- Wibowo ‘Bow’ Arindrarto
Thank you all.
Peter
P.S. You can follow @Biopython on Twitter
—
Checksums for interest/public record:
$ shasum -a 256 biopython-1.72* abc14a111ed89332c902d239f516cc9ab84ab4458b577c61208dc4c20b74 dc83 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 3e8c85d4a3295be598a9e9616adeed 8a4f81bd0452326aaea7bf81cca468 f7c1 biopython-1.72-cp27-cp27m- manylinux1_i686.whl f1b4abd90d0c84ab2c5dab704da1d3 97cf75ee41f72619a1802479c3768a c347 biopython-1.72-cp27-cp27m- manylinux1_x86_64.whl b426a2d858414bed0c25fca155fdf2 7485347ce6f69805db65b8b36ec00a 0f41 biopython-1.72-cp27-cp27mu- manylinux1_i686.whl 71762c193ffc9a1b936dfaa2d456fb 172856f0952090483ee4a84635a1aa 6fe3 biopython-1.72-cp27-cp27mu- manylinux1_x86_64.whl 57a449709df7a47980360ecbd2f195 effc56e9b0253fa0e74fb00b10b447 78e0 biopython-1.72-cp27-cp27m- win32.whl 3d3deb59c3f5d04d41aec443db4e89 dbbdd0bb7749078f91e797935849c8 db48 biopython-1.72-cp27-cp27m-win_ amd64.whl b76241a55a1ba832c2768733fb113e ef1fdfa1d738aa1f84fcdd4ba0b643 2394 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 ad2c72c289561d51f6f7a9ae977e9c d54cd48b575b946421f82ede1ac241 98cb biopython-1.72-cp34-cp34m- manylinux1_i686.whl 3a199d469465c4f3c4c238f688d07b 9bce4f504be73dead6cdf5d36a4772 8fcd biopython-1.72-cp34-cp34m- manylinux1_x86_64.whl 16a99e2462ee5acb6962f3a1d34433 6db58d7b87acf9d5023beb3efe6ebb 47a8 biopython-1.72-cp34-cp34m- win32.whl defd163110d698ea534e470995c68c 519bd56e4e23043ae9dd8b646f2a80 3e5b biopython-1.72-cp34-cp34m-win_ amd64.whl 5882ba8fb87cbbe36d9e5d87c9b8f3 139d503fe7da1023b472760a8122e5 79e6 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 99faabef8c563bf5a9ed80ea677a5f d9edab5c06405a08fe44fb0f5bd4f6 af38 biopython-1.72-cp35-cp35m- manylinux1_i686.whl 539a475c263b68cd1ae3624648090b f1a5d853ec967d450e4cb991e63f72 cb05 biopython-1.72-cp35-cp35m- manylinux1_x86_64.whl 874a3c30bf7287e003e3668b55bd73 a243edb85f4249826cff54b6fe3740 483a biopython-1.72-cp35-cp35m- win32.whl db3517d654c2ca81c57b2e4e534065 0b55055eb3985e5732c5ec668cf701 43f1 biopython-1.72-cp35-cp35m-win_ amd64.whl 2fbfe0f2d7b731b638c41466987cf0 0e36e08502b3db2b2d72beb9cbb790 97e3 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 6d8e56e46cccc38fb8ac026e70f700 528f0d5e6f264d03f9c348fb81dd7e 65b6 biopython-1.72-cp36-cp36m- manylinux1_i686.whl 6d27eb0fda18f2f70661bcd498f2aa 0148ce56953aac094c35d8a12fb826 1482 biopython-1.72-cp36-cp36m- manylinux1_x86_64.whl d3c7ba7b0ffb3dd5132093d4fb2178 2daccc0e41358e5887676c455e1ae8 41c9 biopython-1.72-cp36-cp36m- win32.whl 5e0b830ff270b16abf1f050a8bf473 2c9f2da29d27fdd2be9aeab76b6d08 7919 biopython-1.72-cp36-cp36m-win_ amd64.whl ab6b492443adb90c66267b3d24d602 ae69a93c68f4b9f135ba01cb06d36c e5a2 biopython-1.72.tar.gz 08e1d6b43d974efc3578a5e8eebe6c 118b03feea21b96d964c7e461c5cf5 3c18 biopython-1.72.zip
$ md5sum biopython-1.72* 661d50514eaa8151192b2127f52a8f5e 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