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update with snakemake #80

Merged
merged 126 commits into from
Aug 28, 2017
Merged

update with snakemake #80

merged 126 commits into from
Aug 28, 2017

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RNAer
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@RNAer RNAer commented Aug 25, 2017

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@RNAer
add prodigal rule
678c9be
@RNAer
Merge branch 'master' of github.com:biocore/micronota
07974b6
@RNAer
add rule files for snakemake and delete old cfg files
b6404e2
@RNAer
fix rules and snakefile
8afb7e1
@RNAer
update rules
facd102
@RNAer
update snakefile
8642b03
@RNAer
code up the snakemake cmd
6d5c06d
@RNAer
use snakemake API instead of cmd
bdcc291
@RNAer
update pip/conda requirements
f5f8b19
@RNAer
update each rule to create *.ok file
1502fce
@RNAer
add validate_seq()
2199378
@RNAer
add genetic_code to config
935f2d7 
rm unneccessary parameters
@RNAer
add integrate()
748c554 
other misc changes
@RNAer
update setup.py
728280f 
remove unneccessary param from cli
@RNAer
add minced parser
f41202d
@RNAer
delete bfillings and other unneccessary files
84c4511
@RNAer
add logging config
5cb4e4f
@RNAer
add test for snakemake rules
74d7be1
@RNAer
re-organize files
1ffa55a
@RNAer
update log.cfg
749e3d7
@RNAer
update test_rules
55c9980
@RNAer
move the logger setting
62323e5 
otherwise, it causes problem when running nosetest, although it is fine
to run it separately as a python script.
@RNAer
remove test_config.py
16206d0
@RNAer
clean up minor things
c30252a
@RNAer
add verbose flag
44fa608 
fix .travis.yml
@RNAer
add prodigal parser
00df920
@RNAer
update logging
46e5ecb
@RNAer
remove level setup from log.cfg
5c94a6e
@RNAer
add test for validate_seq()
40ae1e9
@RNAer
redefine output file names
960e7f7
RNAer and others added 18 commits May 11, 2017 17:17
@RNAer
update suffix split to accomandate zipped files
7242e59
@RNAer
allow lowercases for DNA
c3b2814 
update .travis.yaml
@RNAer
add filter_partial_genes
68459f2
@RNAer
provide API function for summarization
f4af6a5
@RNAer
update ci
ccdf41a 
need master branch of scikit-bio
@RNAer
update ci
0654e70 
need master branch of scikit-bio
@RNAer
add quality option to eanble or disable compute quality score
ca85fbb 
update _add_cds_metadata to replace with real seq id for the proteins
@RNAer
add summarize into integrate cmd
ee917db
@qiyunzhu
added summarize function
134a02c
@qiyunzhu
Merge branch 'snakemake' into stats
1af5f71
@qiyunzhu
addressed Zech's comments
7a71bd2
@qiyunzhu
addressed Zech's further comment
8dc6e89
@qiyunzhu
added summarize_iter
565878c
@RNAer
add filter seq cmd
4ab54e8
@RNAer
refactor validate_seq()
0bd7727
@RNAer
update tests
58edeff
@qiyunzhu
removed AA files
688b257
@RNAer
Merge pull request #4 from qiyunzhu/stats
223ae94 
compute summary stats
@tkosciol tkosciol self-requested a review August 25, 2017 23:18
@coveralls
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coveralls commented Aug 25, 2017 •
edited

Coverage Status

Coverage decreased (-19.6%) to 59.322% when pulling 223ae94 on RNAer:snakemake into c1b688b on biocore:master.

tkosciol
tkosciol reviewed Aug 28, 2017
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this PR is unreviewable due to its size.
However, I understand basic mechanisms which are implemented here and they seem reasonable. So, as long as Travis passes, appropriate tests are in place and @RNAer confirms that this exact version works as expected, I can merge.

@coveralls
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coveralls commented Aug 28, 2017 •
edited

Coverage Status

Coverage increased (+1.01%) to 79.915% when pulling cd7a3d6 on RNAer:snakemake into c1b688b on biocore:master.

@RNAer
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RNAer commented Aug 28, 2017

Thanks, @tkosciol . The tests are fixed.

@tkosciol tkosciol merged commit 64031ef into biocore:master Aug 28, 2017
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4 participants
@RNAer @coveralls @tkosciol @qiyunzhu