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  1. May 09, 2022
  2. May 05, 2022
  3. Apr 25, 2022
  4. Mar 22, 2022
  5. Mar 15, 2022
  6. Mar 02, 2022
  7. Jan 21, 2022
  8. Nov 14, 2021
    • Neil P's avatar
      Add defined attribute to Seq (#3779) · 8546c962
      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
      8546c962
  9. Nov 02, 2021
  10. Sep 28, 2021
  11. Sep 13, 2021
  12. Sep 11, 2021
  13. Sep 08, 2021
    • Sebastian Bassi's avatar
      Fix 3696 lcc (#3706) · 44b15e57
      Sebastian Bassi authored
      * Fixing bug #3696. Change LLC log base and first value in list
      * adding change description in NEWS.rst file with DOI
      44b15e57
  14. Sep 07, 2021
    • Damien Goutte-Gattat's avatar
      Fix order of SnapGene join features on reverse strand (#3662) · 119ec9a0
      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.
      119ec9a0
  15. Sep 06, 2021
  16. Sep 03, 2021
  17. Jul 29, 2021
  18. Jul 02, 2021
  19. Jun 22, 2021
  20. Jun 07, 2021
  21. Jun 04, 2021
  22. Jun 03, 2021
  23. May 31, 2021
  24. Mar 23, 2021
  25. Mar 19, 2021
  26. Feb 26, 2021
  27. Feb 20, 2021
  28. Feb 06, 2021
    • Leighton Pritchard's avatar
      Issue 3466 (#3473) · 13e17e90
      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: default avatarLeighton Pritchard <leighton.pritchard@mac.com>
      13e17e90
  29. Dec 04, 2020
  30. Dec 03, 2020
    • mdehoon's avatar
      Add a parser for 2bit files to Bio.SeqIO (#3388) · 41b6f225
      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
      41b6f225
  31. Nov 17, 2020
  32. Nov 09, 2020
  33. Oct 26, 2020
  34. Sep 28, 2020
    • Damien Goutte-Gattat's avatar
      SeqIO/SnapGene: Store feature name in specific qualifier · 05107f5c
      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.
      05107f5c
  35. Sep 19, 2020