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Commits on Sep 16, 2016
  1. Bio.Seq module now has a complement function

    See pull request #938.
    peterjc committed Sep 16, 2016
  2. PEP8

    MarkusPiotrowski committed Sep 16, 2016
Commits on Sep 13, 2016
  1. fix pep8 error

    carlosp420 committed Sep 13, 2016
  2. remove importing unittest2 needed for python2.6

    carlosp420 committed Sep 12, 2016
Commits on Sep 12, 2016
  1. Thank Carlos in NEWS file.

    See pull request #932 and preceding commit.
    peterjc committed Sep 12, 2016
Commits on Sep 11, 2016
  1. README: drop 2.6 from list of supported Python

    As stated in the News, the next version of Biopython 1.69 will not support
    Python 2.6.
    
    This version has also been removed from the Travis configuration file.
    So maybe is good to remove it from the README as well.
    carlosp420 committed Sep 11, 2016
Commits on Sep 3, 2016
  1. NCBI deprecating GI numbers, use accession in QBLAST test

    peterjc committed Sep 3, 2016
  2. Use byte literals rather than _as_bytes

    Could have done this once we dropped Python 2.5, since
    Python 2.6+ including all Python 3 releases supports the
    byte literal notation.
    peterjc committed Sep 3, 2016
  3. Compare .get_raw for index and index_db directly

    This test uncovered a handful of issues with the indexers
    not capturing the raw record length correctly.
    peterjc committed Sep 3, 2016
  4. Re-write the IG indexer to capture raw length

    peterjc committed Sep 3, 2016
  5. IntelliGenetics indexer was returning wrong length

    Looks like it was returning length from the previous record.
    peterjc committed Sep 3, 2016
  6. SeqIO indexing FASTQ raw length wrong for zero-length sequence

    Was missing the blank quality score line in the indexer
    record length in bytes, meaning get_raw as used with
    Bio.SeqIO.index_db was missing the last line.
    
    Spotted via new unit test checking that get_raw
    from Bio.SeqIO.index (using start offset only
    and Bio.SeqIO.index (using start offset and raw
    length of record via indexer) consistent.
    peterjc committed Sep 3, 2016
  7. Fixed minor typos

    peterjc committed Sep 3, 2016
  8. Fix uniprot-xml get_raw via index_db (wrong end point)

    Spotted via new unit test checking that get_raw
    from Bio.SeqIO.index (using start offset only)
    and Bio.SeqIO.index (using start offset and raw
    length if record via indexer) consistent.
    peterjc committed Sep 3, 2016
Commits on Sep 2, 2016
  1. Deprecate taking a string in UniprotIterator

    This was an anomoloy in the SeqIO API.
    peterjc committed Sep 2, 2016
  2. Update comments

    peterjc committed Sep 2, 2016
Commits on Sep 1, 2016
  1. PEP8 whitespace in NEXUS tests

    peterjc committed Sep 1, 2016
  2. Cope with longs in location arguments (Python 2 only)

    Apparently BioSQL on MySQL could return longs rather than
    ints, resulting in a TypeError occuring. See e.g.
    
    http://stackoverflow.com/questions/15206612/dbseqrecord-cannot-access-annotations-features-using-biosql-under-biopython?rq=1
    peterjc committed Aug 29, 2016
Commits on Aug 30, 2016
  1. SeqXmlIterator should define __next__

    It should define __next__ in order that Python consider it to be
    an iterator (and not just an iterable).
    
    It also ought to subclass SequenceIterator which defines __iter__
    in terms of __next__, and provides a stub implementation only of
    __next__
    peterjc committed Aug 30, 2016
  2. PEP8 whitespace

    peterjc committed Aug 30, 2016
  3. Mention NEXUS work in NEWS file.

    Chris Warth is already in the contributors for this release.
    peterjc committed Aug 30, 2016
  4. various Nexus parsing fixes

    - remove '/' from the list of prohibited characters in nexus identifiers.
    - allow ',' in nexus comments on internal nodes.  Perviously ',' was
      allowed in the comments on the whole tree (most encapsulating node)
      but through a quirk in the parser ',' could not appear in the
      comments of internal nodes.
    - add Nexus test cases to check if comment parsing is working as expected.
    Chris Warth committed with peterjc Nov 13, 2015
Commits on Aug 29, 2016
  1. Show new dot-less description in the test output

    Closes GitHub #615.
    peterjc committed Feb 1, 2016
  2. Update the GenBank.Record output to restore trailing dot

    Part of fixing #615
    peterjc committed Feb 1, 2016
  3. fix issue #615

    #615
    ensure that the filed DEFINITION ends with a period as in Genbank
    format specifications.
    bneron committed with peterjc Sep 18, 2015
  4. Thank Chris Warth for the PAML work

    peterjc committed Aug 29, 2016
  5. Long taxa names and testing with PAML v4.8

    Squashed commit of pull request #671, includes docstring
    edits to better match PEP257.
    Chris Warth committed with peterjc Nov 16, 2015
Commits on Aug 28, 2016
  1. Remove unused import (of deprecated module) in FSSP

    peterjc committed Aug 28, 2016
  2. Avoid alphabet-only init warning

    peterjc committed Aug 28, 2016