- May 09, 2022
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Jarrod Millman authored
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- May 05, 2022
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Christian Brueffer authored
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- Apr 25, 2022
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João Rodrigues authored
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João Rodrigues authored
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- Mar 22, 2022
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Manuel Lera Ramirez authored
Should fix #3746. Includes two additional test cases.
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- Mar 15, 2022
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Sean Aubin authored
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- Mar 02, 2022
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Alex Morehead authored
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- Jan 21, 2022
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Markus Piotrowski authored
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Peter Cock authored
Must quote 3.10 to avoid getting Python 3.1
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- Nov 14, 2021
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Neil P authored
* Add defined attribute to Seq - Add "defined" attribute to Seq object that returns true if the Seq contains a fully defined sequence and false if it is unknown or partial - Fixes #3667 * Update run_tests.py to support Python 3.10 - The run_tests.py script assumes that python has a single digit major version and single digit minor version, update to support any size version numbers * Simplify Seq.defined check * Address review comments - Check if data is defined in a more OO way - Update partial data types to be considered defined if they contain a complete sequence
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- Nov 02, 2021
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Erik Whiting authored
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- Sep 28, 2021
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Peter Cock authored
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- Sep 13, 2021
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Peter Cock authored
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- Sep 11, 2021
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Chris Rands authored
typo
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- Sep 08, 2021
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Sebastian Bassi authored
* Fixing bug #3696. Change LLC log base and first value in list * adding change description in NEWS.rst file with DOI
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- Sep 07, 2021
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Damien Goutte-Gattat authored
* SnapGene: Fix ordering of reverse composite features. The locations of the individual segments making up a feature must be added in reverse order when the feature is on the minus strand. * SnapGene: Skip "gap" segments for split features. SnapGene uses a "gap" segment to represent the interval between two parts of a split feature. Such segments must be skipped to build an accurate CompoundLocation for the feature (otherwise the gap segments are interpreted as being part of the feature). * SnapGene: Check for multi-valued qualifiers and split features. When testing the SnapGene parser, check that it correctly handles qualifiers with multiple values and features split in several parts. * Use a "parts" qualifier to represent named subfeatures. SnapGene allows the different parts of a compound feature to have their own name. This is not something we can directly represent in the SeqRecord model, so if a feature part has a name, we translate it to a distinct "misc_feature" in addition to the encompassing compound feature. If a multi-segment feature contains named segments, store the name of those segments in a dedicated "parts" qualifier with the following format: X:name_of_segment_X;Y:name_of_segment_Y Use a 1-based index to identify segments, and for features on the reverse strand, the first segment is the one appearing last.
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- Sep 06, 2021
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Peter Cock authored
See mailing list discussion
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- Sep 03, 2021
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Peter Cock authored
[ci skip]
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- Jul 29, 2021
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Peter Cock authored
Also use generic phrasing about fixing typos.
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- Jul 02, 2021
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Aziz Khan authored
* JASPAR 2018 and onwards return tf_class and tf_family as vector * updated news and contrib
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- Jun 22, 2021
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Fabian Egli authored
Co-authored-by: eglif <fabian.egli@hest.ethz.ch>
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- Jun 07, 2021
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zhuchcn authored
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- Jun 04, 2021
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Fabian Egli authored
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Peter Cock authored
[ci skip]
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João Rodrigues authored
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- Jun 03, 2021
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Peter Cock authored
[ci skip]
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- May 31, 2021
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João Rodrigues authored
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- Mar 23, 2021
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Sergio authored
Added parser for UniProt GOA Gene Product Information (GPI) version 1.2, including sample and test.
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- Mar 19, 2021
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Gert Hulselmans authored
Generate proper count matrix when reading motifs in minimal MEME format by using 'nsites' to calculate the counts from the frequency matrix and rounding the resulting values.
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Gert Hulselmans authored
Updated NEWS: 'pfm-four-rows' scientific notation support.
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- Feb 26, 2021
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Peter Cock authored
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- Feb 20, 2021
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mdehoon authored
* updated NEWS * code * travis * travis * travis
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- Feb 06, 2021
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Leighton Pritchard authored
* fix for issue #3466 The KGML version had incremented to 0.7.2 (see https://www.genome.jp/kegg/xml/ ) but the KGML parser had not been kept up to date. These changes update mentions of KGML v0.7.1 to v0.7.2, and fix the parser so that it produces KGML compliant with the DTD for relation subtype entities. * update NEWS.rst * black reformatting * add test to check download/write/parse KGML roundtrip This test is in response to issues #3465 and #3466 - which noted that the KGML-writing function was out of sync with KGML v0.7.2 Co-authored-by: Leighton Pritchard <leighton.pritchard@mac.com>
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- Dec 04, 2020
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Peter Cock authored
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- Dec 03, 2020
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mdehoon authored
* add test script * add test files * done * travis * travis being obnoxious * remove unnecessary str support * avoid using PyUnicode_New as it's not in pypy * add some documentation * add some documentation * move to a comment to travis can't bitch about it * move to a comment to travis can't bitch about it * documentation update * fix warning * Let's see why 32bit windows is not happy * Let's see why 32bit windows is not happy * check the file descriptor in advance; on Windows, lseek with a closed file descriptor will by default close the application * lseek is fubar on windows * lseek and read apparently are fubar on Windows. Use Python to seek/read, and numpy to keep the code reasonably fast * deal with closed files * travis * more inane stuff from Travis * weird * reverting previous change to the tutorial text * reverting changes to test_SeqIO.py; these are not needed anymore now that twoBit file reading is done via Python * improving speed * using C code for 2bit to sequence conversion * adding missing C code * expand exception * accept formats I and L * release buffer * travis * windows * private * NEWS
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- Nov 17, 2020
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Peter Cock authored
See Bio/Sequencing/Applications/_Novoalign.py and discussion on #3365.
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- Nov 09, 2020
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Peter Cock authored
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- Oct 26, 2020
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Peter Cock authored
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- Sep 28, 2020
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Damien Goutte-Gattat authored
* SnapGene: Store feature name in specific qualifier (#3286). Features in SnapGene files may carry a SnapGene-specific "name" attribute containing a different value from the standard "label" qualifier. If so, we store that name in a dedicated qualifier so that it can be accessed by client code. Thanks to GitHub user @nicolazilio for the bug report. * SnapGene: Update test file. Update the SnapGene sample files to test different combinations of "name" and "label" feature attributes.
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- Sep 19, 2020
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Suyash Gupta authored
* Residue names read from PDB files are now stripped of leading/trailing spaces for compatibility with mmCIF format. * Small optimizations to SeqIO readers depending on PDB/mmCIF files.
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