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https://github.com/multimeric/aaindexer

A Python package for accessing and parsing the AAindex, a collection of amino acid properties and substitution matricies.
https://github.com/multimeric/aaindexer

aaindex amino-acid bioinformatics protein

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A Python package for accessing and parsing the AAindex, a collection of amino acid properties and substitution matricies.

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README 

        

aaindexer

*********



A Python package for accessing and parsing the `AAindex

`_, a collection of amino acid

properties and substitution matricies. You might want this package so

that you can characterise certain amino acid residues, for example to

compare the change in chemical properties caused by a missense

mutation. Some notable features this offers are:



*  Python API *and* CLI with JSON output



*  Detailed test suite



*  Parsing Expression Grammar for parsing AAindex entries that can be

   used independently



*  Automatic handling of some idiosyncrasies of the AAindex format



*  AAindex itself is not included, avoiding any breaches of the

   license



Installation

************



::



   pip install aaindexer



Or, if you’re a super cool `poetry `_

user:



::



   poetry add aaindexer



CLI

***



aaindexer

=========



Scrapes a single aaindex database, and prints the result to stdout. A

progress bar is shown via stderr.



.. code:: shell



   aaindexer [OPTIONS] DATABASE_NUMBER



-[ Options ]-



``--pretty, --no-pretty``



   If pretty (the default), pretty print the JSON, with newlines and

   indentation.



-[ Arguments ]-



``DATABASE_NUMBER``



   Required argument



Python API

**********



**class aaindexer.AaindexRecord**



   A single record from a single aaindex database



   ``accession: str``



      Record accession, e.g. ``"ANDN920101"``



   ``authors: Optional[str]``



      Authors for the source publication, as a single string, e.g.

      ``"Andersen, N.H., Cao, B. and Chen, C."``



   ``comment: Optional[str]``



      Additional comments



   ``correlation: Optional[dict[str, Optional[float]]]``



      A dictionary of correlations between this record and others in

      the same database. The dictionary is indexed by the record

      accession number. e.g. ``{ "ROBB760101": 0.874, "QIAN880106":

      0.846 }``



   ``description: str``



      Record description, as a string, e.g. ``"alpha-CH chemical

      shifts (Andersen et al., 1992)"``



   ``index: Optional[dict[str, Optional[float]]]``



      A dictionary indexed by amino acid 1-letter codes, where the

      values are amino acid properties described in this record. e.g.

      ``{"A": 0.68, "R": -0.22 }``



   ``journal: Optional[str]``



      Journal for the source publication, e.g. ``"Biochem. and

      Biophys. Res. Comm. 184, 1008-1014 (1992)"``



   ``matrix: Optional[dict[str, dict[str, Optional[float]]]]``



      A dictionary of dictionaries. The first and second index are

      both amino acid 1-letter codes, defining up a substitution

      matrix between the two amino acids. e.g. ``{ "A": { "A": 3.0 },

      "R": { "A": -3.0, "R": 6.0 }``. Note that if matrix[X][Y] is not

      defined, then matrix[Y][X] (the reverse) will be.



   ``pmid: Optional[str]``



      PubMed identifier, e.g. ``"PMID:1575719"``



   ``title: Optional[str]``



      Title of the source publication, e.g. ``"Peptide/protein

      structure analysis using the chemical shift index method:

      upfield alpha-CH values reveal dynamic helices and aL sites"``



**aaindexer.scrape_database(index)**



   Scrapes an aaindex database, and returns it as plain text



   :Parameters:

      **index** (*int*) – The number of the database to return (1-3)



   :Returns:

      The aaindex database contents



   :Return type:

      str



**aaindexer.scrape_parse(index, progress=False)**



   Scrapes an aaindex database and parses the result



   :Parameters:

      *  **index** (*int*) – The number of the database to return

         (1-3)



      *  **progress** – If true, show progress



   :Return type:

      list[`aaindexer.models.AaindexRecord

      <#aaindexer.AaindexRecord>`_]



Citation

********



Please cite the original AAindex paper if you are using this package

or the raw data: Kawashima, S. & Kanehisa, M. AAindex: Amino Acid

index database. Nucleic Acids Research 28, 374 (2000).



Development

***********



Clone the repo, and then:



*  ``poetry install`` to install development dependencies



*  ``poetry run pytest test.py`` to run tests



*  ``poetry run sphinx-build . _build -b rst`` to build the readme,

   then ``_build/index.rst README.rst`` to replace the old readme