The Transcripts_Plots script is designed to generate publication‑quality gene model plots from transcript annotation data found in GTF files. It extracts and plots the exon structure and/or coding sequence (CDS) of a given transcript, supporting both single‐transcript and multi‐transcript modes. The script also accommodates different display modes—either plotting the introns to their full scale or compressing them for easier viewing.
Transcript models are invaluable in computational analyses, as they aid in conceptual representation and facilitate comparisons among gene models across isoforms, paralogs, and orthologs. However, existing tools do not readily support plotting transcript models by themselves. To address this gap, we developed a tool that extracts transcript model information from a genome annotation file (e.g., GTF) and generates a corresponding transcript model plot.
- Author: Rodolfo Aramayo
- Work_Email: raramayo@tamu.edu
- Personal_Email: rodolfo@aramayo.org
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
- v1.0.3
Code_Overview.md
Mini_Tutorial.md
--------------------------------------------------------------------------------
FLAG: "--transcript"
REQUIRED: Yes
FORMAT: Alphanumeric String
DEFAULT: No default
HELP: Transcript ID
NOTES: Script was tested with Ensembl transcripts IDs
--------------------------------------------------------------------------------
FLAG: "--gtf"
REQUIRED: Yes
FORMAT: Alphanumeric String
DEFAULT: No default
HELP: GTF file (required with '--transcript')
NOTES: Script was tested with Ensembl GTF files
--------------------------------------------------------------------------------
FLAG: "--file"
REQUIRED: Yes
FORMAT: Text file
DEFAULT: No default
HELP: Text file with multiple transcripts and GTF paths (2 tab-delimited columns)
NOTES: Text file containing multiple transcripts and their associated GTF files paths and names
Name_Example: Ensembl_multiple_genes_transcripts_list.txt
File_Content: No Header
ENST00000278224<tab>Homo_sapiens.GRCh38.113.chr.gtf<$>
ENST00000380525<tab>/path/to/other/gtf_file/ENSG00000110619_GTF.gtf<$>
ENST00000397111<tab>Homo_sapiens.GRCh38.113.chr.gtf<$>
--------------------------------------------------------------------------------
FLAG: "--select"
REQUIRED: No
FORMAT: Alphanumeric String
CHOICES: 'exons', 'CDS', 'both'
DEFAULT: 'exons'
HELP: Select feature to be plotted: 'exons', 'CDS', or 'both'
--------------------------------------------------------------------------------
FLAG: "--exon_color"
REQUIRED: No
FORMAT: Hexadecimal Color
CHOICES: https://g.co/kgs/CNRQC6y
DEFAULT: '#305c96'
HELP: Color for Exons
--------------------------------------------------------------------------------
FLAG: "--CDS_color"
REQUIRED: No
FORMAT: Hexadecimal Color
CHOICES: https://g.co/kgs/CNRQC6y
DEFAULT: '#b38d1b'
HELP: Color for Coding Exons
--------------------------------------------------------------------------------
FLAG: "--full_scale"
REQUIRED: No
FORMAT: Alphanumeric String = '--full_scale'
CHOICES: Omitting the flag: == 'False'
Providing the flag: == 'True'
ACTION: store_true
DEFAULT: 'False'
HELP: Plot entire region to scale
Otherwise introns are compressed uniformly
--------------------------------------------------------------------------------
FLAG: "--no_transcript_label"
REQUIRED: No
FORMAT: Alphanumeric String = '--no_transcript_label'
Omitting the flag: == 'True'
Providing the flag: == 'False'
ACTION: store_false
DEFAULT: 'True'
HELP: Do not print the transcript label above the plot
--------------------------------------------------------------------------------
FLAG: "--labels"
REQUIRED: No
FORMAT: Alphanumeric String
CHOICES: 'none', 'full'
DEFAULT: 'none'
HELP: Label features with numbers
Only the first and last are labeled
--------------------------------------------------------------------------------
FLAG: "--format"
REQUIRED: No
FORMAT: Alphanumeric String
CHOICES: 'pdf', 'png', 'svg'
DEFAULT: 'pdf'
HELP: Output file format
--------------------------------------------------------------------------------
FLAG: "--dpi"
REQUIRED: No
FORMAT: Integer
DEFAULT: '300'
HELP: Resolution (dpi) for PNG output file
--------------------------------------------------------------------------------
FLAG: "--dynamic_resize"
REQUIRED: No
ACTION: store_true
CHOICES: Omitting the flag: == 'False'
Providing the flag: == 'True'
DEFAULT: 'False'
HELP: Dynamically adjust figure size to match drawn content
Eliminates extra whitespace
--------------------------------------------------------------------------------
FLAG: "--figsize"
REQUIRED: No
#_Of_Arguments: 2
FORMAT: Float
DEFAULT: '10, 8'
HELP: Figure size in inches (width height)
--------------------------------------------------------------------------------
FLAG: "--transcript_fontsize"
REQUIRED: No
FORMAT: Integer
DEFAULT: '18'
HELP: Font size for the transcript label
--------------------------------------------------------------------------------
FLAG: "--output"
REQUIRED: No
FORMAT: Alphanumeric
DEFAULT: 'Transcripts_Plots_dir_Run01'
HELP: Output directory name
If provided and exists, a numeric suffix is added (e.g., Test01)
--------------------------------------------------------------------------------
FLAG: "-v", "--version"
REQUIRED: No
ACTION: version
FORMAT: Alphanumeric
HELP: Show program version's number and exit
--------------------------------------------------------------------------------
FLAG: "-h", "--help"
REQUIRED: No
ACTION: help
FORMAT: Alphanumeric String
HELP: show this help message and exit
--------------------------------------------------------------------------------
| Name | URL |
|---|---|
| Python3 | https://www.python.org/downloads/ |
| Matplotlib | https://matplotlib.org/ |
| https://pypi.org/project/matplotlib/ |
| Distributor ID | Description | Release | Codename |
|---|---|---|---|
| Apple, Inc. | Apple M1 Max | 15.3.1 | Sequoia |
- Script was tested with:
| Python Version | matplotlib | pandas | seaborn |
|---|---|---|---|
| 3.8.20 | 3.7.5 | 2.0.3 | 0.13.2 |
| 3.9.21 | 3.9.4 | 2.2.3 | 0.13.2 |
| 3.10.16 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.11.11 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.12.9 | 3.10.1 | 2.2.3 | 0.13.2 |
| 3.13.2 | 3.10.1 | 2.2.3 | 0.13.2 |
Transcripts_Plots_Python
Transcripts_Plots_Python_Issues
@misc{RN161,
author = {Aramayo, Rodolfo},
title = {Transcripts_Plots_Python},
publisher = {CERN Data Centre & InvenioRDM},
month = {2025-03-03},
keywords = {Bioinformatics
comparative genomics
ensembl
gene annotation
genome annotation
genome browsers},
DOI = {10.5281/zenodo.14962604},
url = {https://doi.org/10.5281/zenodo.14962604},
year = {2025},
type = {Dataset}
}