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czbiohub-sf / orpheum

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.
MIT License
18 stars 4 forks source link

CLI for k-mer homology #12

Closed olgabot closed 4 years ago

olgabot commented 4 years ago

Formalize these notebooks: https://github.com/czbiohub/kh-analysis/pull/4 to put here: https://github.com/czbiohub/nf-ortholog/pull/1

FYI @bluegenes

codecov-io commented 4 years ago

Codecov Report

Merging #12 into master will increase coverage by 4.76%. The diff coverage is 40.85%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #12      +/-   ##
==========================================
+ Coverage   29.46%   34.22%   +4.76%     
==========================================
  Files          19       19              
  Lines         862      894      +32     
==========================================
+ Hits          254      306      +52     
+ Misses        608      588      -20
Impacted Files Coverage Δ
khtools/common.py 36.84% <ø> (ø) :arrow_up:
khtools/jupyter_utils.py 50% <ø> (ø) :arrow_up:
khtools/idf.py 30.76% <ø> (ø) :arrow_up:
khtools/os_utils.py 83.33% <0%> (ø) :arrow_up:
khtools/holoviews.py 0% <0%> (ø) :arrow_up:
khtools/s3_utils.py 27.77% <0%> (ø) :arrow_up:
khtools/__init__.py 100% <100%> (ø) :arrow_up:
khtools/commandline.py 84.61% <100%> (+2.79%) :arrow_up:
khtools/ensembl.py 17.91% <100%> (+17.91%) :arrow_up:
khtools/sequence_encodings.py 100% <100%> (ø) :arrow_up:
... and 11 more

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olgabot commented 4 years ago

Using this instead: https://github.com/czbiohub/kh-tools/pull/22/