CHANGELOG.md

Change Log

Unreleased

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Closed issues:

• Installation and running problems #74
• mac brew install does not work. #63

Merged pull requests:

• fix readme and add to codecov #75 (ssjunnebo)
• using six for urllib.parse for support of python 3 #73 (sachalau)
• update LICENSE and AUTHORS #72 (ssjunnebo)

v1.1.4 (2016-11-11)

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Merged pull requests:

• Include XX line between features (FT) and sequence (SQ) #70 (peterjc)
• Unescape percent encoding from GFF3, then line wrap #69 (peterjc)

v1.1.3 (2016-11-10)

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Merged pull requests:

• More wrapping tests; Fix ignored test #68 (peterjc)

v1.1.2 (2016-11-10)

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Closed issues:

• Sequence header SQ line can exceed 80 characters #65

Merged pull requests:

• EMBL files wrap at 80 characters, not 79 #67 (peterjc)

v1.1.1 (2016-11-09)

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Closed issues:

• Change PROKKA to Prokka in repo description #64
• linuxbrew recipe needs updating #62

Merged pull requests:

• Sq exceeds 80 #66 (andrewjpage)

v1.1.0 (2016-09-21)

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Implemented enhancements:

• I have added this to my brew repo (updated to 1.0.9) #59

Fixed bugs:

• Failure to install on Biolinux #38

Merged pull requests:

• fix typos #61 (satta)
• Docker file #60 (andrewjpage)

v1.0.9 (2016-05-24)

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Merged pull requests:

• check codon start is a number #57 (andrewjpage)

v1.0.8 (2016-05-23)

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Merged pull requests:

• Remove colour tag #56 (andrewjpage)
• Remove double quoting #55 (andrewjpage)
• Break on hyphen #54 (andrewjpage)

v1.0.6 (2016-05-06)

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v1.0.5 (2016-05-03)

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Implemented enhancements:

• Format for listing authors not defined #45

Fixed bugs:

• Should unescape %2C in GFF column 9 as comma in EMBL #50
• Document versions of Python supported #42

Merged pull requests:

• Avoid breaking long words in product attributes #53 (peterjc)
• Un-escape %2C to comma etc for GFF3 to EMBL #52 (peterjc)
• Ec dash #49 (andrewjpage)

v1.0.3 (2015-12-10)

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Fixed bugs:

• Long author lists break instead of line wrapping #46

Merged pull requests:

• Make publication arguments a little more explicit #48 (peterjc)

v1.0.2 (2015-12-10)

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Closed issues:

• self.assertItemsEqual is Python 2.7 only #43
• Non-standard indentation of Python code #41
• Python 3 support #40

Merged pull requests:

• Wrap publication lines #47 (andrewjpage)
• Add note that it only works on Python 2.7 #44 (bewt85)
• Use Python 3 ready exception, print, etc #39 (peterjc)

v1.0.1 (2015-09-02)

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Closed issues:

• v1.0.0 vs v1.0 #36

Merged pull requests:

• Complete genome naming #37 (andrewjpage)
• README.md: Fix a spelling mistake gff3toemble #35 (sjackman)

v1.0.0 (2015-07-13)

Closed issues:

• OSX and dlylib #33
• Does this cope with Prokka GFF3 files ok? #23

Merged pull requests:

• Add TravisCI Support (and fix setup.py) #34 (bewt85)
• case insensitive hypo search #32 (andrewjpage)
• get the version of the script with --version #31 (andrewjpage)
• Empty product hypo protein #30 (andrewjpage)
• Update README and version #29 (bewt85)
• gff3toembl on Mac OS X #28 (satta)
• Add usage example to readme #26 (bewt85)
• Default "publication" to include today's date #25 (bewt85)
• Refactor / rewrite / remove convert.py #24 (bewt85)
• Duplicate entries #22 (andrewjpage)
• intermediate gff prefix to suffic #21 (andrewjpage)
• sort and tidy gff files with GT #20 (andrewjpage)
• Revert rna feature translate #19 (andrewjpage)
• No trans table for rna #18 (andrewjpage)
• Convert type for 16s #17 (andrewjpage)
• Unknown function #16 (andrewjpage)
• replace unknown with uncharacterised #15 (andrewjpage)
• extra dot #14 (andrewjpage)
• passes java validator #13 (andrewjpage)
• Update format #12 (andrewjpage)
• version #11 (andrewjpage)
• Made EC number values unique #10 (aslett1)
• Create Chromosome.txt file #9 (andrewjpage)
• update version #8 (andrewjpage)
• Add chrom name to source #7 (andrewjpage)
• Split lines on words, fix headers and references #6 (andrewjpage)
• fix input param names #5 (andrewjpage)
• convert inference to db_xref #4 (andrewjpage)
• rename script #3 (andrewjpage)
• Working script for converting #2 (andrewjpage)
• initial working version #1 (andrewjpage)