refactor

Author: telatin

.gitignore

@@ -132,5 +132,5 @@ the_real_final_input/
 .DS_Store
 .vscode/
 .idea/
-*.md
+./*.md
 !README.md

paper/.gitignore

@@ -0,0 +1 @@
+paper/.md

paper/paper.md

@@ -0,0 +1,88 @@
+---
+title: 'nomenclator: a Python package for the automated generation of Latin binomials for Bacterial and Archaeal genera'
+tags:
+  - Python
+  - microbiology
+  - taxonomy
+  - nomenclature
+  - bioinformatics
+authors:
+  - name: Andrea Telatin
+    orcid: 0000-0001-7619-281X
+    affiliation: 1
+affiliations:
+  - name: Quadram Institute Bioscience, Norwich, UK
+    index: 1
+date: 28 October 2025
+bibliography: paper.bib
+---
+
+# Summary
+
+`nomenclator` is a Python package that automates the creation of linguistically valid Latin binomials for bacterial and archaeal taxa, based on the "Great Automated Nomenclator" script [@Pallen2021].
+Bacterial nomenclature requires Latin or Latinized names that conform to the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and Latin grammar [@Parker2019, @Oren2019].
+The tool generates taxonomic names by combinatorially concatenating roots from 
+Latin and Greek starting from two Excel files containing curated lists of roots to be combinatorially assembled into genus and species names. 
+
+
+
+# Statement of Need
+
+The exponential growth in microbial species discovery through culturomics, genomics, and metagenomics has created an urgent need for millions of new taxonomic names—far exceeding the capacity of manual expert-driven nomenclature.
+`nomenclator` addresses this bottleneck by providing pre-generated, grammatically correct names that can be used "off the shelf" as needed.
+
+Creating valid taxonomic names is challenging because it requires:
+
+1. **Classical language expertise**: Names must follow Latin grammar rules with proper gender agreement and declension
+2. **ICNP compliance**: The nomenclature code contains 65 rules and numerous recommendations
+3. **Manual quality control**: Each name requires expert review, creating a significant bottleneck
+
+
+# Implementation and Features
+
+## Installation
+
+The package can be installed via `pip`:
+
+```bash
+pip install nomenclator
+```
+
+## Tools
+
+`GAN` is implemented in pure Python (3.8+) with minimal dependencies.
+The package exports these CLI tools:
+
+- `gan-genus`: Generates genus names based on user-defined parameters (number of names, roots to use, etc.)
+- `gan-init`: Initializes a project directory with necessary files and templates
+- `xls2tsv`: Converts Excel files with taxonomic data into TSV format for further processing
+
+## Example input and output
+
+An example of the input Excel file structure is shown below:
+
+| Language | Gender | Part | Word        | Root      | Definition                           | Explanation |
+|----------|--------|------|-------------|-----------|--------------------------------------|-------------|
+| L.       | masc.  | n.   | admissarius | admissari | a stallion used for breeding         | horses      |
+| Gr.      | masc.  | n.   | Arion       | ariono    | a mythical horse that could speak    | horses      |
+| Gr.      | masc.  | n.   | Balios      | Balio     | a mythical horse                     | horses      |
+| L.       | masc.  | n.   | caballus    | caballi   | a horse                              | horses      |
+
+The programme's output can be saved as HTML or PDF files. An example is:
+
+* **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.
+* **Admissaristercoradaptatus** - Etymology: *L. masc. n. admissarius*, a stallion used for breeding; *L. neut. n. stercus*, excrement; *L. masc. n. adaptatus*, something adapted; `Admissaristercoradaptatus`: a microbe of the faeces of horses.
+* **Admissaristercorihabitans** - Etymology: *L. masc. n. admissarius*, a stallion used for breeding; *L. neut. n. stercus*, excrement; *L. masc. n. habitans*, an inhabitant; `Admissaristercorihabitans`: a microbe of the faeces of horses.
+# Acknowledgments
+
+This software originated from research conducted with Mark J. Pallen and Aharon Oren, published in *Trends in Microbiology* [@pallen2021], where it demonstrated the concept of mass nomenclature generation for prokaryotic taxonomy.
+
+# Funding
+
+The author gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); this research was funded
+by the BBSRC Core Capability Grant BB/CCG2260/1
+and by the BBSRC Institute Strategic Programme Microbes and Food Safety 
+BB/X011011/1 and its constituent project 
+BBS/E/QU/230002C.
+
+# References

tests/all.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+set -euo pipefail
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
+
+INPUT=$DIR/../input_test/
+OUTPUT=$DIR/../output/
+SCRIPTS=$DIR/../scripts/
+bold=$(tput bold)
+normal=$(tput sgr0)
+R1="$INPUT"/test_input_genera_part1.xlsx
+R2="$INPUT"/test_input_genera_part2.xlsx
+R3="$INPUT"/test_input_genera_part3.xlsx
+
+for i in $R1 $R2 $R3;
+do
+  echo "$bold * Validating: $(basename $i)$normal"
+  if [ -e "$i" ]; then
+    $SCRIPTS/gan-validate.py -p -i "$i"
+  else
+    echo "ERROR: $i not found."
+    exit 1
+  fi
+done
+
+echo "$bold * Genera: three roots$normal"
+set -x pipefail
+mkdir -p $OUTPUT/
+$SCRIPTS/gan-genus.py -1 "$R1" -2 "$R2" -3 "$R3" -o $OUTPUT/ > $OUTPUT/genera_3.html
+set +x
+
+echo "$bold * Genera: two roots$normal"
+$SCRIPTS/gan-genus.py -1 "$R1" -2 "$R3"  -o $OUTPUT/ > $OUTPUT/genera_2.html
+

tests/make_suppl.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+set -euxo pipefail
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
+JOIN="of"
+DATASETS="$DIR/../the_real_final_input"
+GAN="$DIR/../scripts/gan-genus.py"
+VAL="$DIR/../scripts/gan-validate.py"
+for i in "$DATASETS"/*; 
+do
+  B=$(basename $i); 
+  echo $B; 
+  for FILE in "$i"/[1-3].xlsx; do
+  	$VAL -t -i "$FILE" > "$FILE.validation.log" 2>&1
+  done
+done
+
+
+for i in "$DATASETS"/*; 
+do
+  B=$(basename $i); 
+  echo $B; 
+  if [[ -e "$i/1.xlsx" && -e "$i/2.xlsx" && -e "$i/3.xlsx" ]]; then
+    $GAN -1 "$i/1.xlsx" -2 "$i/2.xlsx" -3 "$i/3.xlsx" --connector "$JOIN" -o "$i/" --prefix "${B/_/-}"
+  elif [[ -e "$i/1.xlsx" && -e "$i/2.xlsx" ]]; then
+  	$GAN -1 "$i/1.xlsx" -2 "$i/2.xlsx"                --connector "$JOIN" -o "$i/" --prefix "${B/_/-}"
+
+  fi
+done
+