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Commits on Nov 26, 2015
  1. @peterjc
  2. @peterjc
  3. @peterjc

    Fix use of posix.popen(...) without an import.

    peterjc committed
    Spotted while browsing the report.
    The posix module documentation suggests using sys.popen(...)
    instead, of course that is now deprecated in favour of subprocess,
    so this would need further work for Python 3.
    Or could we just remove the xbbtools entirely?
  4. @peterjc

    PEP8 comment spacing

    peterjc committed
  5. @peterjc
  6. @peterjc
  7. @peterjc

    Fixed some typos in comment

    peterjc committed
Commits on Nov 24, 2015
  1. @peterjc

    Thank Joao for Entrez POST work

    peterjc committed
    See GitHub pull request #608
  2. @peterjc

    Merge pull request #608 from jotomicron/patch-1

    peterjc committed
    Added a POST option to the esearch util
  3. @peterjc
  4. @peterjc

    Merge branch adding label_colors arg to Phylo.draw

    peterjc committed
    See GitHub pull request #672 and branch  'phylo-draw-tip-colors'
Commits on Nov 23, 2015
  1. @peterjc

    Allow multiple dots in GenBank location external reference names

    peterjc committed
    e.g. AL358792.24.1.166931:3274..3461 and more complex compound locations like
    both from
    I can't find anything in
    to say these locations are invalid, nor in Feature Location of
    Closes #677 which was
    originally raised as
  2. @peterjc

    Fix accidentally inclusive GenBank location regex.

    peterjc committed
    Note ord(z) = 122, while ord(Z) = 90, so the old version wasn't
    an invalid regular expression, but it was accidentally allowing
    punctuation characters 91 to 96.
Commits on Nov 22, 2015
  1. @peterjc

    Add general note about handles to Bio.Entrez docstring.

    peterjc committed
    Also updated the copyright statement.
Commits on Nov 21, 2015
  1. @peterjc
  2. @wwood
  3. @wwood
Commits on Nov 19, 2015
  1. @bamueh
Commits on Nov 18, 2015
  1. @bamueh

    Changed doc string

    bamueh committed
  2. @bamueh
Commits on Nov 16, 2015
  1. @peterjc

    Insert note about Python versions into NEWS file.

    peterjc committed
    This was in the Biopython 1.66 release annoucement, makes sense
    to have it in the NEWS file too.
  2. @peterjc Tests/ directory path changes

    peterjc committed
    I intended to include this in the earlier commit today.
    See discussion on GitHub #669.
  3. @peterjc
  4. @peterjc

    Use Tests/ as working directory in

    peterjc committed
    This would have helped with the initial problem reported
    on GitHub issue #669, where lots of the tests failed due
    to relative paths not being found.
    TODO: Should we instead error if not already in Tests/ ?
  5. @peterjc

    Fix comment placment

    peterjc committed
Commits on Nov 10, 2015
  1. @jotomicron

    Refactored the decision to POST into _open

    jotomicron committed
    As per the discussion on PR #608 [1], and NCBI guidelines [2], we need to
    request queries through POST when the number of UIDs is 200+ or the length of
    the query is 1000+ characters. The reasoning is as follows:
    - NCBI asks that requests with 200+ UIDs are made using POST
    - UIDs can have up to 7 characters, plus another one for the comma
    - With 200 UIDs, the parameter id=... occupies 1800 characters. To err on the
      safe side, it's better to set the threshold on 1000
    Now, EFetch, EPost, ESummary and ELink are also made through POST when 200+
    UIDs are used, and ESearch, EGQuery and ESpell are made through POST when the
    request would result in a long URL.
    [1] #608
Commits on Nov 7, 2015
  1. @peterjc

    Thank Chris Warth for PAML fix.

    peterjc committed
    See GitHub pull request #665
Commits on Nov 6, 2015
  1. @peterjc

    Minor update to NEWS

    peterjc committed
  2. @peterjc

    PEP8 tweak

    peterjc committed
Commits on Nov 5, 2015
  1. split options ate first '='

    chris warth committed
    - parsing a codeml option file like this fails,
        seqfile = /purifying/noindel/pop=1000/sample_aln_fixed.fa
      because there are '=' characters in the path.
      Only consider the first '=' as seperating name from value.
Commits on Nov 3, 2015
  1. @peterjc
  2. @peterjc
  3. @peterjc
  4. @lennax @peterjc
  5. @dkoppstein @peterjc
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