Skip to content

Latest commit

 

History

History
121 lines (85 loc) · 4.64 KB

documentation.md

File metadata and controls

121 lines (85 loc) · 4.64 KB
Raw

GAN 1.0

Installation

GAN is a Python script requiring Python (>3.6), IPython, itertools, pandas (>= 1.0), xlrd (>=1.2.0).

To install the required dependencies, an option is to use the Miniconda package manager (https://docs.conda.io/en/latest/miniconda.html), and create a new environment using the bundled environment.yaml file to create a new environment to be used to run the bundled scripts.

Commands:

# Create the environment (run it once)
conda env create -f environment.yml

# Activate the environment to use the scripts
conda activate gan

Usage

The repository comes with two scripts:

  • gan-validate.py - to perform a check of the Excel input files
  • gan-genus.py - to combine two or more Excel files

gan-genus.py

usage: gan-genus.py [-h] -1 FIRST -2 SECOND [-3 THIRD] -o OUTDIR [-p PREFIX] [-c CONNECTOR] [-v]

Generate bacterial genera with Excel input

optional arguments:
  -h, --help            show this help message and exit
  -1 FIRST, --first FIRST
                        First Excel file in "GAN" format
  -2 SECOND, --second SECOND
                        Second Excel file in "GAN" format
  -3 THIRD, --third THIRD
                        Third Excel file in "GAN" format
  -o OUTDIR, --outdir OUTDIR
                        Output directory
  -p PREFIX, --prefix PREFIX
                        Output basename [default: 'gan']
  -c CONNECTOR, --connector CONNECTOR
                        String connecting the explanatory strings [default: 'of']
  -v, --verbose         Increase output verbosity

The program requires two or three Excel tables, to be supplied with the -1, -2 and -3 arguments, respectively.

The program requires an output directory to be specified (via -o), and optionally an output "basename" prefix (via -p).

The repository comes with small test files to check that the program is working properly. From the base directory of the repository:

mkdir test_output
./scripts/gan-genus.py -1 ./test/table1.xlsx -2 ./test/table2.xlsx -o ./test_output

This will produce three files in the test_output directory:

  • gan.html (HTML formatted text)
  • gan.json (computer friendly output, in JSON format)
  • gan.tex (LaTeX list, requiring an additional config.tex from the docs directory)

Input

Each input file is an Excel file with at least one workbook (any other workbook is discarded). An empty template is provided in input_test/template.xlsx.

It should contain these columns (in any order):

  • Language (L. for Latin, Gr. for Greek ...)
  • Gender (masc., fem., neut. or masc./fem. or blank)
  • Part (n. for noun, etc.)
  • Word (the original word)
  • Root (the root extracted from the word. This will be combined and must be unique in the file)
  • Definition (definition of the word used to produce the etymology)
  • Explanation (this is concatenated with a connector, for example of)

Small example:

Language Gender Part Word Root Definition Explanation
L. masc. n. admissarius admissari a stallion used for breeding horses
Gr. masc. n. Balios Balio a mythical horse horses
L. masc. n. caballus caballi a horse horses

Output

JSON format

The JSON object is an array of elements, each element is a dictionary having as key the compound name (e.g. _ Admissaristercoradaptatus_) and as value an array of tuples in the form of (type, value), where type specifies how to render the value. Some examples:

  • [ "glossary", "L." ]
  • [ "separator", " " ]
  • [ "italic", admissarius ]

HTML format

An HTML formatted list of compound words and their etymology.

Each item is provided as:

Admissaristercoricola -- Etymology: L. masc. n. admissarius, a stallion used for breeding; L. neut. n. stercus, excrement; N.L. masc./fem. n. cola, an inhabitant; Admissaristercoricola: a microbe of the faeces of horses.

LaTeX format

A LaTeX source that can be compiled to produce a PDF document. It requires a config.tex file (supplied in the docs/ directory) and can be used to produce the PDF with this command:

pdflatex gan.tex

To install a LaTeX package, on Ubuntu (requires ~5 Gb of space):

sudo apt install texlive-full