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Next release#70

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averagehat merged 122 commits intomasterVDBWRAIR/bio_bits:masterfrom devVDBWRAIR/bio_bits:devCopy head branch name to clipboardJan 4, 2016

+2,807-126

Commits

Commits on May 27, 2015

• Added initial ctleptop script #22

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• Test data for ctleptop #22

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Commits on Jun 10, 2015

• Added a test code #22

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• commented unnecssary routines #22

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• added ctleptop to setup.py #22

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Commits on Jun 17, 2015

• Updated the final tabular print out #22

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Commits on Jul 20, 2015

• Added multiple fasta test file #24

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Commits on Jul 22, 2015

• bugfix

  

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Commits on Jul 28, 2015

• support multi-seq-file

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Commits on Aug 3, 2015

• Working version for multifasta

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• Commented testing lines

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Commits on Aug 4, 2015

• Cleaned the code, working for multiple fastafile

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Commits on Aug 6, 2015

• Updated the setup.py #24

  

  demis001

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• Updated the ctleptopy, support multifasta #24

  

  demis001

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• Updated the test_ctleptopy, support multifasta #24

  

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Commits on Aug 10, 2015

• updated the test script #24

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• Updated main script #24

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• Updated the test script #24

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• Updated the requirment file #24

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• Added the diverse test data #24

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Commits on Aug 11, 2015

• updated the test_ctleptop.py #24

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• Merged two test file with different complexity #24

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• Updated test_ctleptop.py still 43% coverage #24

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Commits on Aug 12, 2015

• Increased test coverge to 43 #24

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Commits on Aug 13, 2015

• Mock main function #24

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Commits on Aug 14, 2015

• Added additional test #24

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• added script for finding genese with degenerate bases

  

  Panciera

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Commits on Aug 19, 2015

• degen.py (for MAAPs) complete

  

  Panciera

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• Merge branch 'dev' of https://github.com/VDBWRAIR/bio_pieces into dev

  averagehat

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Commits on Aug 20, 2015

• added CSV/tab-seperatred file support

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• fixed tab support and external interface

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• fixed imap -> map import for py3

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• skip Genbank download test so travis won't fail

  averagehat

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• initial commit

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• adding more compatibility

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• fixed compatibility of degen for py26

  averagehat

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• fixed funcy python 3/2 issue

  averagehat

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• Merge pull request #48 from VDBWRAIR/compat

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• added docs for degen

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• code cleaning

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• Merge branch 'dev' of https://github.com/VDBWRAIR/bio_pieces into compat

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• Merge pull request #49 from VDBWRAIR/degen-docs

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Commits on Aug 21, 2015

• Update degen.rst

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• added degen to console scripts

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• Added help message #24

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• Merge remote branch 'upstream/dev' into maaps

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• Added function to accept list of degen positions for maaps

  averagehat

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• Added (optional) degen positions to ctleptop output

  averagehat

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• moved mostly completed code to bio_pieces

  necrolyte2

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• fixing python3 issues and replacing pathdiscov references

  necrolyte2

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• Coverage for main function

  necrolyte2

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• Consolidated some code, added tests for main, added script to setup.py

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• Removed unwanted args and changed arg to blast_exe

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• new version of diamond requires -a. Fixed bad last commit

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• Addresses #50

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• Adding docs. Adding fail test to test travis email notification

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• removing test test_fail

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• Updated docs [skip ci]

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• Merge pull request #46 from VDBWRAIR/parallel_blast

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• bare-bones test for ctleptop

  averagehat

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• various fixes

  averagehat

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• fixed incorrect imports

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• Update requirements.txt

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• code cleaning

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• fix filepath

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• added zip

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• reverted travis

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• Merge branch 'dev' of https://github.com/VDBWRAIR/bio_pieces into maaps

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• Merge branch 'maaps' of https://github.com/VDBWRAIR/bio_pieces into maaps

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Commits on Aug 26, 2015

• fixes problem listed in PR #52 with AA index

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Commits on Aug 28, 2015

• changed diamond call such that it outputs the results to standard out after it runs since it uses daa format

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Commits on Aug 31, 2015

• Closes #53. Also ensures that optional arguments are not duplicate of static args. parallel_diamond improvements

  necrolyte2

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• run now prints command it is running. All commands now use run so they print

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• Removed unnecessary print statements

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• Fixed compat import issue for python3

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• small blurp about how diamond is being run

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• removed has_duplicate_args

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• changed from -a to --daa because the way command is printed does not handle short args. TODO

  necrolyte2

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• Merge pull request #59 from VDBWRAIR/parallel_blast

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Commits on Oct 28, 2015

• replaced ctletop test file for pybot test

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• changed pybot name

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• fixed float/integer division error in py3

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Commits on Oct 30, 2015

• Merge pull request #52 from VDBWRAIR/maaps

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Commits on Nov 10, 2015

• Copyright file

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• Update .travis.yml

  necrolyte2

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• renamed using find/sed all bio_pieces. Renamed directory

  necrolyte2

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• Merge branch 'rename-project-i60' of https://github.com/VDBWRAIR/bio_pieces into rename-project-i60

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• test/import for deprecated calls

  necrolyte2

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Commits on Nov 12, 2015

• before dev merging

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• forgot this

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• Merging rename-project-i60 branch with dev

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• find/sed to replace bio_pieces with bio_bits

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• deprecation import

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• deprecation warning

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• Update __init__.py

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• fixed tests

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Commits on Nov 13, 2015

• Merge pull request #69 from VDBWRAIR/rename-project-i60

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Commits on Nov 18, 2015

• bumped to 1.2.0

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• change ctleptop to degen_regions in console_scripts

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Commits on Dec 30, 2015

• Changelog for 1.2.0. fixed installation doc. fixed ctleptop robot test

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• manually merging in parallel_blast fix. Closes #61. Closes #45

  necrolyte2

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• fixing up dgen docs

  necrolyte2

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• added documentation for degen_regions. Added tests to ensure genbank accession downloads and has same output. Added test to ensure tab file works

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• removing redundant function call

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• Adding 5'UTR and 3'UTR to output for degen_regions

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• implemented coding region

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• removing file

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• add plot_muts

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• added plot_muts to console scripts

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• added range_regex dep.

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• plot_muts documentation

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Commits on Dec 31, 2015

• fixing ctleptop tests and removing isGap function which is no longer used

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• Fixed pybot tests for ctleptop. Made it prettier to look at too

  necrolyte2

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• fixed documentation for plot_muts. Fixed incorrect console script name. Added exception for better error message if invalid fasta identifier

  necrolyte2

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• fixed legend

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• Create query.fas

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• Create refs.fas

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• doc now uses test files

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• Update changelog

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• added idexception back

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• plot muts with corrected legend and example png image for docs

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Commits on Jan 4, 2016

• Fixed beast_checkpoint docs. [skip ci]

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