Skip to content
This repository

Apr 18, 2014

  1. Peter Cock

    More useful error message from Bio.TogoWS.search_count(...)

    This seems to be returning XHTML for several people over
    multiple operating systems, and may be due to a change or
    temporary problem with TogoWS.
    authored April 18, 2014
  2. Peter Cock

    Warn if SFF files are missing null padding at end

    Thanks for Martin Mokrejš for sample data and emails about this issue.
    authored April 18, 2014
  3. Peter Cock

    Catch and warn if SFF files are missing null padding at end

    Thanks for Martin Mokrejš for sample data and emails about this issue.
    authored April 18, 2014

Apr 09, 2014

  1. Peter Cock

    Clarify argument for BgzfBlocks in docstring.

    Follows feedback on the mailing list.
    authored April 09, 2014
  2. Peter Cock

    Context manager (with statement) support in Bio.bgzf

    authored April 09, 2014

Apr 01, 2014

  1. Wibowo Arindrarto

    Add test for QueryResult ordering

    authored April 01, 2014

Mar 29, 2014

  1. Eric Talevich

    NexusIO: write trees with only 1 trailing semicolon, not 2

    Newick.Writer.to_string already appends a semicolon, so we don't need to add
    another in the NEXUS output template.
    authored March 29, 2014

Mar 28, 2014

  1. Peter Cock

    Restore old behaviour of molecular_weight with generic alphabet

    Thanks to Markus Piotrowski pointing out I'd broken backward compatibility.
    See #235 on GitHub.
    authored March 28, 2014

Mar 27, 2014

  1. Peter Cock

    Remove three unit test *output* files

    authored March 27, 2014
  2. Peter Cock

    Stricter type checking in molecular_weight; Adding doctests

    authored March 27, 2014
  3. Peter Cock

    Thank Markus for sequence mass/weight work (pull request #235)

    authored March 27, 2014
  4. Markus Piotrowski

    Bugfix for DNA/RNA masses; enhanced molecular_weight function

    In Bio.Data.IUPACData:
    - corrected masses for monophosphate nucleotides in unambiguous_dna_weights and unambiguous_rna_weights (most values where too high by a mass of 16 Da)
    - added two dictionaries with monoisotopic masses for monophosphate nucleotides (monoisotopic_unambiguous_dna_weights and monoisotopic_unambiguous_rna_weights)
    - added average and monisotopic masses for selenocysteine and pyrrolysine in protein_weights and monoisotopic_protein_weights
    
    Rewrote method molecular_weight to:
    - correct the calculation (sum masses of sequence elements and substract 18 Da for each formed bond)
    - allow mass calculation for RNA and protein sequences
    - allow mass calculation for double stranded nucleic acids
    - use  more precise masses for water
    
    Updated test_ProtParam.py with new results due to changed masses in IUPACData
    
    Also now using Python 3 print style for docstrings
    authored September 02, 2013 peterjc committed March 27, 2014
  5. Peter Cock

    Use assertEqual in unit test, not assert statement.

    Also remove unused variable.
    
    This test is failing for me with Python 3.4 on Windows XP (32 bit),
    likely due to some global warning filter issue and/or new core
    warning.
    authored March 27, 2014
  6. Peter Cock

    Deprecate function quick_FASTA_reader

    authored March 27, 2014
  7. Peter Cock

    Remove deprecated Bio.UniGene.UniGene module (HTML parser)

    authored March 27, 2014
  8. Peter Cock

    Remove deprecated legacy BLAST wrappers from Bio.BLAST.Applications

    authored March 27, 2014
  9. Peter Cock

    Remove deprecated legacy BLAST functions blastall, blastpgp, rpsblast

    authored March 27, 2014
  10. Peter Cock

    Now testing under Python 3.4

    We'll have this on the buildbot server shortly, while
    Python 3.4 support on Travis-CI.org is expected soon.
    authored March 27, 2014
  11. Peter Cock

    Remove deprecated class InterlacedSequenceIterator from SeqIO

    authored March 27, 2014
  12. Peter Cock

    Remove deprecated Bio.Search module

    authored March 27, 2014
  13. Peter Cock

    Remove deprecated Bio.HotRand module

    authored March 27, 2014
  14. Peter Cock

    PEP8 tweaks, print functions

    authored March 27, 2014
  15. Peter Cock

    Make these full Biopython deprecation warnings, not just pending.

    Also remove duplicate imports
    authored March 27, 2014
  16. Wibowo Arindrarto

    Remove redundant str(...) in print statements

    authored December 21, 2012 peterjc committed March 27, 2014
  17. Wibowo Arindrarto

    Remove last remnants of Seq.tostring and deprecate it

    authored December 19, 2012 peterjc committed March 27, 2014
  18. Wibowo Arindrarto

    Note down 'homology' -> 'similarity' rename in NEWS

    authored March 27, 2014
  19. Wibowo Arindrarto

    Rename 'homology' in SearchIO aln_annotation attributes to 'similarity'

    authored March 27, 2014
  20. Wibowo Arindrarto

    Remove unused import

    authored March 27, 2014

Mar 24, 2014

  1. Peter Cock

    More updated NCBI DTD files.

    authored March 24, 2014
  2. Zhaorong Ma

    Update Seq.py

    Fix the docstring of Seq().count() and MutableSeq().count().
    authored March 24, 2014

Mar 21, 2014

  1. Peter Cock

    Fix bytes vs unicode error when missing DTD

    authored March 21, 2014

Mar 20, 2014

  1. Wibowo Arindrarto

    Display similarity character in HSPs only when it's a string

    authored March 21, 2014
  2. Wibowo Arindrarto

    Update exonerate parser to handle dna2protein model

    authored March 21, 2014
  3. Tiago Antao

    wMerge branch 'master' of github.com:biopython/biopython

    authored March 20, 2014
  4. Tiago Antao

    simcoal -> fastsimcoal

    authored March 20, 2014
Something went wrong with that request. Please try again.