pretextannotate 1.1.0

A package to annotate a pretext snapshot with size and chromosome information

pretextannotate

PretextAnnotate is a script originally written by Karen van Niekerk (Sanger GRIT) in order to add chromosome annotations to a PNG image produced by PretextSnapshot.

/src/fonts/OpenSans-Regular.ttf - Open Sans font file used for text rendering. Font file is taken from https://fonts.google.com/specimen/Open+Sans/ and is licensed under Open Font License.

original_scripts - Contains the original scripts used in this project, this is simply for archiving and reference purposes.

Installation

git clone https://github.com/sanger-tol/pretextannotate.git

cd pretextannotate

pip install .

Coming soon

pip install pretextannotate

Usage

To make full use of the script (and politeness to NCBI) you must set the environment variables: ENTREZ_EMAIL ENTREZ_API_KEY

You can generate your own API keys by creating an account on https://www.ncbi.nlm.nih.gov/account/ with your ORCID.

pretextannotate -h

pretextannotate \\
    --pretext_file src/tests/ilDryDodo1.1_normal_FullMap.png \\
    --output ./ \\
    --prefix HELLO \\
    --context_dict '{"accession": "GCA_965178025.1"}'

Context is a dictionary input containing the type of accession and the GCA accession number of the specific assembly.

Expected output

With the input pretext snapshot:

As well as the arguments used in the Usage section.

The output should be a PNG, gif and tif file resembling:

There will also be a pretextannotation.log file containing, in this case:

2026-02-12 12:55:46,100 [INFO] [Pretext Annotation] Starting Pretext Annotation
2026-02-12 12:55:46,100 [INFO] [Pretext Annotation] PretextSnapshot: src/tests/ilDryDodo1.1_normal_FullMap.png | WITH | context_dict: {"accession": "GCA_965178025.1"}
2026-02-12 12:55:46,100 [INFO] [Pretext Annotation] Input Snapshot Image is src/tests/ilDryDodo1.1_normal_FullMap.png
2026-02-12 12:55:46,100 [INFO] [Pretext Annotation] Output will be saved at .//HELLO_annotated_pretext.png
2026-02-12 12:55:46,100 [INFO] [Pretext Annotation] Starting Pretext Annotation Process
2026-02-12 12:55:46,470 [INFO] [Pretext Annotation] Adjusted font size: 60 for 31 chromosomes
2026-02-12 12:55:47,355 [INFO] [Pretext Annotation] Saved labelled PNG → .//HELLO_annotated_pretext.png
2026-02-12 12:55:47,783 [INFO] [Pretext Annotation] Converted .//HELLO_annotated_pretext.png → .//HELLO_annotated_pretext.tif, .//HELLO_annotated_pretext.gif
2026-02-12 12:55:47,783 [INFO] [Pretext Annotation] Converted to TIFF & GIF → .//HELLO_annotated_pretext.tif, .//HELLO_annotated_pretext.gif

ToDo:

• Graphs to right side
  • Telomere, gap, coverage, repeats, GC?
• Tests
• Workflow for PyPi Push