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Commits on Nov 29, 2016
  1. Added ExPASy Cellosaurus parser with tests

    Squashed commit from pull request #983 with merge conflict
    fixed and NEWS entry reworded (by Peter).
    stevemmarshall committed with peterjc Nov 7, 2016
  2. Fill in a couple of GitHub URLs in CONTRIB file

    peterjc committed Nov 29, 2016
  3. Thank Adrian and Brandon for PAML fix.

    See pull request #1012 and issue #483.
    peterjc committed Nov 29, 2016
  4. Record missing data in Bio.Phylo.PAML.codeml

    Squashed commit from pull request #1012, fixes #483.
    
    The codeml parser parses now all site parameters of a pairwise codeml analysis.
    
    Thanks to Brandon Invergo for his input and review.
    alpae committed with peterjc Nov 29, 2016
  5. Avoid writing output files under Tests/ directory.

    Partly addresses issue #1013
    peterjc committed Nov 29, 2016
  6. Avoid accidentally checking in Doc/examples/other_trees.nwk

    peterjc committed Nov 29, 2016
Commits on Nov 28, 2016
Commits on Nov 25, 2016
  1. Remove left-over handle.close()

    peterjc committed Nov 25, 2016
  2. Can now use context manager with gzip and bz2

    We've dropped Python 2.6 since I first wrote these examples.
    peterjc committed Nov 25, 2016
  3. Fix bzip2 SeqIO example under Python 3

    Note bz2.open was added in Python 3.3
    peterjc committed Nov 25, 2016
  4. Fix example inconsistency

    peterjc committed Nov 25, 2016
  5. Fix gzip file mode

    This closes issue #1009.
    peterjc committed Nov 25, 2016
Commits on Nov 24, 2016
  1. Thank Aaron for KEGG documentation update

    See pull request #660 (overdue for merging), and preceeding
    commits turning these examples into Tutorial doctests.
    peterjc committed Nov 24, 2016
  2. adding example for KEGG.Enzyme.read()

    arosenfeld committed with peterjc Oct 30, 2015
  3. Belatedly update copyright year. Tweak docstring formatting.

    peterjc committed Nov 24, 2016
  4. Clean up indentation issues

    (Patch manually resuced and rebased from pull request #945).
    biologyguy committed with peterjc Sep 28, 2016
  5. Fix test in test_SeqIO_features.py

    This line was accidentally removed in cleanup commit
    4940bc7
    peterjc committed Nov 24, 2016
  6. Update NEWS with recent GenBank/EMBL/IMGT work

    peterjc committed Nov 24, 2016
  7. NCBI now has spaces in GenBank DBLINK lines.

    Closes GitHub issue #998
    peterjc committed with peterjc Nov 23, 2016
  8. Explicitly record EMBL/GenBank molecule type

    peterjc committed with peterjc Nov 16, 2016
Commits on Nov 23, 2016
  1. Mention EMBL and IMGT work in NEWS

    peterjc committed Nov 23, 2016
  2. Update IMGT parser for new IPD-IMGT/HLA database files.

    After v3.16.0, IPD-IMGT/HLA adopted a new format ID line.
    
    Closes GitHub issue 988.
    peterjc committed Nov 23, 2016
  3. Handle EMBL patent files from KIPO

    peterjc committed Nov 23, 2016
  4. Sample of Patent Protein Sequence data from KIPO

    This is the first 596 lines from this file:
    ftp://ftp.ebi.ac.uk/pub/databases/patentdata/kipo_prt.dat.gz
    
    Dated 2015-12-17
    
    Note mixture of STANDARD and standard in the ID line.
    peterjc committed Nov 23, 2016
  5. Fix string/bytes issue in error message

    peterjc committed Nov 23, 2016
  6. Update test_SeqIO_online.py for NCBI GI changes

    peterjc committed Nov 23, 2016
  7. Update TogoWS tests for NCBI GI changes

    (Right now some of the TogoWS tests are failing
    but for unrelated reasons.)
    peterjc committed Nov 23, 2016