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Commits on Nov 23, 2009
  1. Adding Seq object ungap method developed on one of my git branches pl…

    peterjc committed Nov 23, 2009
    …us explicit UnknownSeq support (see mailing list)
  2. Deprecating the obsolete module Bio.listfns(most of this is covered b…

    peterjc committed Nov 23, 2009
    …y Python itself nowadays)
  3. Remove Bio.pairwise2.py dependency on obsolete Bio.listfns (which use…

    peterjc committed Nov 23, 2009
    …d a naive Python implementation anyway, not C code)
Commits on Nov 20, 2009
  1. More doctests in Bio/Seq.py

    peterjc committed Nov 20, 2009
Commits on Nov 19, 2009
Commits on Nov 18, 2009
Commits on Nov 17, 2009
  1. Adding final tests for the MAST parser

    mdehoon
    mdehoon committed Nov 17, 2009
Commits on Nov 16, 2009
  1. Starting work on the BLAST chapter of the tutorial. Moving online sec…

    peterjc committed Nov 16, 2009
    …tion to the start (simpler for beginners)
  2. Should have all BLAST+ command line arguments supported now, except s…

    peterjc committed Nov 16, 2009
    …oft_masking and use_index where it is unclear from the documentation if they should be a 'switch' or an 'option' taking a boolean argument
  3. Adding more missing NCBI BLAST+ options (guided by the new unit test)…

    peterjc committed Nov 16, 2009
    …, should be everything except for some blastn options
  4. Fixed typo in new warning.

    peterjc committed Nov 16, 2009
  5. Update Bio.ExPASy.get_sprot_raw() to use URL http://www.uniprot.org/u…

    peterjc committed Nov 16, 2009
    …niprot/XXX.txt as per http://www.expasy.ch/expasy_urls.html since the old URL http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?XXX is currently returning FASTA format. See report via mailing list. This fixes test_SeqIO_online.py
Commits on Nov 15, 2009
  1. Adding a more explicit test for the MAST parser; skipping the parser …

    mdehoon
    mdehoon committed Nov 15, 2009
    …code that does not work yet
Commits on Nov 13, 2009
Commits on Nov 11, 2009
  1. More SeqRecord addition tests

    peterjc committed Nov 11, 2009
  2. Fixed a boundary condition and negative slice coordindates problem in…

    peterjc committed Nov 11, 2009
    … feature handling for SeqRecords