nRCA support in SeqUtils CodonUsage #1692
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added normRelativeCodonAdaptationIndex class to support nRCA index computations [O'Neill, Or and Erill (PLoS One. 2013 Oct 7;8(10):e76177)] defines a complete class equivalent to the existing CodonAdaptationIndex class that supports CAI index computations https://www.ncbi.nlm.nih.gov/pubmed/24116094 https://www.ncbi.nlm.nih.gov/pubmed/20453079
updated test script to test the newly introduced normRelativeCodonAdaptationIndex class
added FASTA files for reference set (refset_Sharp.fas) and test data (sample_genes.fas)
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| 'GLU': ['GAG', 'GAA'], | |||
| 'TYR': ['TAT', 'TAC']} | |||
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| # DNA bases that can occupy each codon position | |||
| CodonBases = {'A' : 0, 'C' : 0, 'G' : 0, 'T' : 0} | |||
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Defining this as a module level variable does not seem ideal. There is a risk of the end user altering it etc.
I think it would be better to define these dictionaries where you do CodonBases.copy() within those methods.
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| class normRelativeCodonAdaptationIndex(object): | ||
| """A normalized Relative Codon Adaptation index implementation. |
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Style wise we try to follow PEP257 for our docstrings, which means a single line summary then a blank line. The rest of the docstring indentation should match the opening quote (i.e. four spaces indented here).
This would fix the flake8 style warnings like:
D208 Docstring is over-indented
D205 1 blank line required between summary line and description
See the CONTRIBUTING.rst file for more about how to run flake8 locally.
| self._codon_count(fasta_file) | ||
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| # compute total number of codons | ||
| total_codons = sum(self.codon_count.values()) + 0.0 |
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I assume the plus 0.0 is to turn this from an integer into a float, in order to avoid integer division under Python 2.
It might be cleaner to import the Python 3 style division?
from __future__ import division
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| # if no index is set or generated, the default ErillLabEcoliIndex will | ||
| # be used. | ||
| if self.index == {}: |
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Stye wise, I think if not self.index: considered more Pythonic.
| # from CaiIndices import SharpIndex # you can save your dictionary in this file. | ||
| # X.SetCaiIndex(SharpIndex) | ||
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| infilename = 'sample_genes.fas' |
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This should be relative to the Tests/ directory:
infilename = 'CodonUsage/sample_genes.fas'
| # X.SetCaiIndex(SharpIndex) | ||
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| infilename = 'sample_genes.fas' | ||
| outfilename = 'nRCA_test_output.csv' |
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This would ideally be a temp file, e.g. via import tempfile, rather than generating output in the Tests/ folder.
This pull request addresses issue #1688
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