althonos / pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
https://pyrodigal.readthedocs.org
GNU General Public License v3.0
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Implement customization of the minimum gene size #11

Closed althonos closed 2 years ago

althonos commented 2 years ago

The minimum gene size can now be set when creating a OrfFinder, and will then be used in the train and find_genes methods.

codecov[bot] commented 2 years ago

Codecov Report

Merging #11 (ba1d5a4) into main (a9b6800) will increase coverage by 0.30%. The diff coverage is 98.48%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main      #11      +/-   ##
==========================================
+ Coverage   96.24%   96.55%   +0.30%     
==========================================
  Files          11       12       +1     
  Lines         533      580      +47     
==========================================
+ Hits          513      560      +47     
  Misses         20       20              
Flag Coverage Δ
CPython 96.55% <98.48%> (+0.30%) :arrow_up:
Linux 96.55% <98.48%> (+0.30%) :arrow_up:
OSX 93.27% <96.96%> (+0.59%) :arrow_up:
PyPy 93.96% <84.84%> (-1.03%) :arrow_down:
Windows 96.55% <98.48%> (+0.30%) :arrow_up:
v3.10 96.55% <98.48%> (+0.30%) :arrow_up:
v3.5 96.28% <98.46%> (+0.32%) :arrow_up:
v3.6 96.46% <98.46%> (+0.31%) :arrow_up:
v3.7 96.46% <98.46%> (+0.31%) :arrow_up:
v3.8 96.55% <98.48%> (+0.30%) :arrow_up:
v3.9 96.55% <98.48%> (+0.30%) :arrow_up:

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Impacted Files Coverage Δ
pyrodigal/tests/test_connection_scorer.py 77.38% <75.00%> (ø)
pyrodigal/__init__.py 100.00% <100.00%> (ø)
pyrodigal/_version.py 100.00% <100.00%> (ø)
pyrodigal/tests/test_genes.py 100.00% <100.00%> (ø)
pyrodigal/tests/test_nodes.py 100.00% <100.00%> (ø)
pyrodigal/tests/test_orf_finder.py 100.00% <100.00%> (ø)
pyrodigal/tests/test_sequence.py 100.00% <100.00%> (ø)

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