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Downloads](https://img.shields.io/pypi/dm/codonpair)\n[![DOI](https://data.caltech.edu/badge/77872126.svg)](https://data.caltech.edu/badge/latestdoi/77872126)\n\ncodonpair\n=========\n\n`codonpair` calculates codon pair score and codon pair bias. CPS\nvalues are identical to those produced by the perl script from\nDimitris Papamichail (`cps_perl` directory) and, presumably,\nused in the following work: \n\n    Virus attenuation by genome-scale changes in codon pair bias.\n    Coleman JR1, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S.\n    Science. 2008 Jun 27;320(5884):1784-7. doi: 10.1126/science.1155761.\n    https://www.ncbi.nlm.nih.gov/pubmed/18583614\n\n\n## Installation\n\nEither, clone the repo and install with pip\n\n```shell\ngit clone git@github.com:smsaladi/codonpair.git\npip install ./codonpair\n```\n\nOr... have pip handle the details:\n\n```shell\npip install git+git://github.com/smsaladi/codonpair@master#codonpair\n```\n\nAll dependencies should be checked for and, if necessary, installed\nautomatically by `pip`.\n\n\n## Usage\n\nInitialize a `codonpair.CodonPair` object by specifying a list of reference sequences\n`CodonPair.from_sequences`, from a named reference `CodonPair.from_named_reference`,\na reference file `CodonPair.from_reference_file`,\nor simply providing a `pd.DataFrame` with codon counts to `CodonPair`.\n\nThe following named references are recognized/bundled with this package.\n\n* `E. coli` (BL21 DE3)\n* `S. pneumoniae` (TIGR4)\n* `cps_perl` -  the reference file provided with the perl implementation\n\nThe default constructor `CodonPair()` uses the `E. coli`.\n\n\nThen calculate the codon pair score for a provided sequence with `CodonPair.cpb`\nwhich returns a dictionary with the\n\n* total codon pair score `total_cps` - the sum of the values of each codon pair\n* the number of codons `n_pair` - excluding codon pairs not found in the reference\n* the codon pair bias `cpb` - `total_cps/n_pair`\n\nFor one-off calculations, `codonpair.calc_cpb` can be used directly\nfor with the sequence of interest (calling the default constructor under the hood).\n\n```python\nimport codonpair\ncp = codonpair.CodonPair.from_named_reference('E. coli')\ncp.cpb(\"ATGATCCCCTTACAACATGGACTGATCCTCGCGGCAATCTTATTCGTTCTTGGCTTAACC\")\n```\n\nFor convenience, the executable `cps` installed into the path by pip:\n\n```bash\ncps test.fasta \u003e test.scores.txt\n```\n\nSee `CodonPair.write_reference` to write codon pair counts for a reference set to\nthe filename provided to be used with future calculations.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmsaladi%2Fcodonpair","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmsaladi%2Fcodonpair","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmsaladi%2Fcodonpair/lists"}