fix: expanded README.md to indicate file formats and seperate execution from testing subcommands; minor code refactoring

Author: donovan-h-parks

README.md

@@ -1,57 +1,71 @@
 # gTranslate
 
-**gTranslate** is a machine learning-based command-line tool designed to automatically detect and predict the genetic translation table (GTT) used in prokaryotic genomes. 
-
-By analyzing specific sequence features—such as coding density differences, Trp ratios, and Gly ratios—`gTranslate` utilizes advanced classifiers to accurately distinguish between different genetic codes, particularly focusing on the identification of recoding events associated with Translation Tables 11, 4 (UGA=Trp), and 25 (UGA=Gly).
+**gTranslate** is a machine learning-based command-line tool for predicting the translation table (TT) used by prokaryotic genomes. By analyzing specific sequence features — such as coding density differences, Trp ratios, and Gly ratios — `gTranslate` can accurately distinguish between the genetic codes associated with reassignment of the UGA stop codon, i.e. translation tables 11 (standard prokaryotic code), 4 (UGA=Trp), and 25 (UGA=Gly).
 
 ## Features
 
-* **Automated Table Detection:** Rapidly predict the correct genetic translation table for single genomes or large batches.
+* **Automated Table Detection:** Rapidly predict the correct translation table for a single genome or large batches of genomes.
 * **Interactive Visualizations:** Generate dynamic HTML dashboards to explore the feature space used by the classifiers.
 
+## Installation
+
+... TBD ...
+
 ## Usage
 
-gTranslate is operated via four primary subcommands: `detect_table`, `generate_plot`, `test`, and `check_install`.
+gTranslate is operated via two subcommands: `detect_table` and `generate_plot`.
 
 You can view the general help menu at any time:
 ```bash
 gtranslate -h
 ```
 
-### 1. `detect_table`
-The core pipeline for detecting the genetic translation table in prokaryotic organisms. You must provide input genomes either via a directory or a batch file.
+### Detect table
+The core pipeline for detecting the translation table used by prokaryotic organisms. You must provide input genomes either via a directory or a batch file.
 
 **Basic Usage:**
 ```bash
-# Process a directory of FASTA files
+# Process a directory of genomic FASTA files
 gtranslate detect_table --genome_dir /path/to/genomes --out_dir /path/to/output
 
-# Process genomes defined in a batch file
+# Process genomic FASTA files defined in a batch file
 gtranslate detect_table --batchfile genomes.tsv --out_dir /path/to/output
 ```
 
-### 2. `generate_plot`
-Generates an interactive HTML dashboard to visually explore the features (e.g., Coding Density Difference, amino acid ratios) used for GTT prediction. 
+The file provided to `--batchfile` is a two-column, tab-separated values (TSV) file that indicates the path to the genomic FASTA file and the desired genome identifier, e.g.:
+```
+/example/path/GCF_001729785.1_ASM172978v1/GCF_001729785.1.fna.gz      G001729785
+/a/different/path/GCF_043834535.1.fna.gz    G043834535
+...
+```
+
+### Generate plot (optional)
+Generates an interactive HTML dashboard to visually explore the features (e.g., coding density difference, amino acid ratios) used by gTranslate to predict the translation table. 
 
 **Basic Usage:**
 ```bash
 gtranslate generate_plot --feature_file features.tsv --output_file dashboard.html
 ```
 
-### 3. `test`
-Runs the built-in test suite on bundled genomic data to validate that the GTT detection pipeline is functioning correctly on your system.
+The file `features.tsv` provided to `--feature_file` is generated by the `detect_table` command.
 
-**Basic Usage:**
-```bash
-gtranslate test --cpus 4
-```
-*Note: If `--out_dir` is not specified, the test will securely execute in a temporary directory.*
+## Testing
+
+Validation that gTranslate has been installed correctly and is operating as expected can be done using the `check_install` and `test` subcommands:
 
-### 4. `check_install`
+### Check installation
 Verifies your installation and ensures that all required dependencies and reference data files are correctly configured and present.
 
 **Basic Usage:**
 ```bash
 gtranslate check_install
 ```
 
+### Test operation of gTranslate
+Runs the built-in test suite on bundled genomic data to validate that gTranslate is functioning correctly on your system.
+
+**Basic Usage:**
+```bash
+gtranslate test --cpus 4
+```
+*Note: If `--out_dir` is not specified, the test will securely execute in a temporary directory.*

gtranslate/tbl_predictor.py

@@ -23,7 +23,7 @@
 from gtranslate.external.prodigal import Prodigal
 from gtranslate.files.prodigal.tln_table_summary import TranslationSummaryFile, TranslationSummaryFileRow
 from gtranslate.files.featurefile import FeatureFile
-from gtranslate.tools import tqdm_log,symlink_f
+from gtranslate.tools import tqdm_log, symlink_f
 
 
 class TablePredictor(object):

gtranslate/tools.py

@@ -16,6 +16,7 @@
 from gtranslate.biolib_lite.seq_io import read_fasta
 
 order_rank = ["d__", "p__", "c__", "o__", 'f__', 'g__', 's__']
+
 ##################################################
 ############MISC UTILITIES########################
 ##################################################
@@ -244,4 +245,3 @@ def __exit__(self, exc_type, exc_val, exc_tb):
 
     def __del__(self):
         self.tqdm.close()
-