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Commits on Oct 3, 2016

• Thank Steve for his GenBank work

  peterjc

  committed
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• Replace all single quotes with double

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  biologyguy

  authored and

  peterjc

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• Decorate static methods and return dummy data as tuple

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  biologyguy

  authored and

  peterjc

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• Reduce line lengths and rename 'in_format' variable

  

  biologyguy

  authored and

  peterjc

  committed
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• Tidy up test file for PEP8 compliance

  

  biologyguy

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  peterjc

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Commits on Sep 29, 2016

• Turn SFF assert into ValueError, fixes the file's self-test

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  peterjc

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• Thank Vincent for Bio.SwissProt doctest; run doctest.

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  peterjc

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• Move Bio/SwissProt/__init__.py selftest to doctest

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  vincentdavis

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Commits on Sep 28, 2016

• Thank Emmanuel Noutahi for AlignInfo pseudo_count work

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  peterjc

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• Add pseudo count support for information content computation (minor edit) (#942)

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  maclandrol

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Commits on Sep 26, 2016

• TravisCI: Install paml and phyml

  peterjc

  committed
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Commits on Sep 16, 2016

• Bio.Seq module now has a complement function

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  peterjc

  committed
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• PEP8

  MarkusPiotrowski

  committed
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• Add 'complement(seq) to Seq module and add tests for this

  MarkusPiotrowski

  committed
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Commits on Sep 13, 2016

• fix pep8 error

  carlosp420

  committed
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• remove importing unittest2 needed for python2.6

  carlosp420

  committed
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Commits on Sep 12, 2016

• Thank Carlos in NEWS file.

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  peterjc

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Commits on Sep 11, 2016

• README: drop 2.6 from list of supported Python

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Commits on Sep 3, 2016

• NCBI deprecating GI numbers, use accession in QBLAST test

  peterjc

  committed
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• Use byte literals rather than _as_bytes

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  peterjc

  committed
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• Compare .get_raw for index and index_db directly

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  peterjc

  committed
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• Re-write the IG indexer to capture raw length

  peterjc

  committed
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• IntelliGenetics indexer was returning wrong length

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  peterjc

  committed
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• SeqIO indexing FASTQ raw length wrong for zero-length sequence

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  peterjc

  committed
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• Fixed minor typos

  peterjc

  committed
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• Fix uniprot-xml get_raw via index_db (wrong end point)

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  peterjc

  committed
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Commits on Sep 2, 2016

• Deprecate taking a string in UniprotIterator

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  peterjc

  committed
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• Use a handle in UniProt XML indexer, not a string

  peterjc

  committed
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• Update comments

  peterjc

  committed
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Commits on Sep 1, 2016

• PEP8 whitespace in NEXUS tests

  peterjc

  committed
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• Cope with longs in location arguments (Python 2 only)

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  peterjc

  committed
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Commits on Aug 30, 2016

• SeqXmlIterator should define __next__

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  peterjc

  committed
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• Clarify developer-centric comments for Bio.SeqIO iterators

  peterjc

  committed
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• Clarify docstring and follow PEP257

  peterjc

  committed
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• PEP8 whitespace

  peterjc

  committed
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