https://github.com/rustcodepro/toxannotator
rustic tox annotator for comparative genomics
https://github.com/rustcodepro/toxannotator
bioinformatics deep-learning deep-neural-networks genome-annotation toxgenomics
Last synced: 14 days ago
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rustic tox annotator for comparative genomics
- Host: GitHub
- URL: https://github.com/rustcodepro/toxannotator
- Owner: rustcodepro
- License: mit
- Created: 2025-11-28T20:23:59.000Z (about 2 months ago)
- Default Branch: main
- Last Pushed: 2025-12-07T20:05:03.000Z (about 2 months ago)
- Last Synced: 2025-12-13T15:27:12.834Z (about 2 months ago)
- Topics: bioinformatics, deep-learning, deep-neural-networks, genome-annotation, toxgenomics
- Language: Rust
- Homepage:
- Size: 86.9 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# toxannotator
- a toxdb annotator for genomic comparison for comparative genomics.
- ready to use tables for comparative analysis.
- genomic comparison and annotation plotters.
```
cargo build
```
```
_____ _ _
|_ _| ___ __ __ __ _ _ __ _ __ ___ | |_ __ _ | |_ ___ _ __
| | / _ \ \ \/ / / _` | | '_ \ | '_ \ / _ \ | __| / _` | | __| / _ \ | '__|
| | | (_) | > < | (_| | | | | | | | | | | (_) | | |_ | (_| | | |_ | (_) | | |
|_| \___/ /_/\_\ \__,_| |_| |_| |_| |_| \___/ \__| \__,_| \__| \___/ |_|
A toxodb annotator.
************************************************
Gaurav Sablok,
Email: codeprog@icloud.com
************************************************
Usage: toxannotator
Commands:
protein-compare Only compare protein coding
protein-compare-seq-command Compare protein coding coordinates and sequences also
protein-plotter Plot the protein coding regions
protein-tensor Prepare the protein tensor for the machine and deep learning
extract-seq plot the specific ids information
comparem-rna compare mRNA annotations
compare-fasta-gff compare fasta and gff for the same and different ids and sequences
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
```
Only compare protein coding
Usage: toxannotator protein-compare
Arguments:
path to the first gff file
path to the second gff file
Options:
-h, --help Print help
toxannotator protein-compare ./testfiles/a1.gff ./testfiles/b1.gff 4
commonggenes-same-strand.txt
TGME49_200010 TGME49_200010 2245476 2245476 2249210 2248187 - -
GeneName Start1 Start2 End1 End2 Strand1 Strand2 Start Difference End Difference
TGME49_200010 2245476 2245476 2249210 2248187 - - 0 1023
```
```
Compare protein coding coordinates and sequences also
Usage: toxannotator protein-compare-seq-command
Arguments:
path to the first gff file
path to the second gff file
fasta1 file
fasta2 file
threads
Options:
-h, --help Print help
```
```
Plot the protein coding regions
Usage: toxannotator protein-plotter
Arguments:
input file 1
input file 2
threads
Options:
-h, --help Print help
toxannotator protein-plotter ./testfiles/a1.gff ./testfiles/b1.gff 4
```
```
Prepare the protein tensor for the machine and deep learning
Usage: toxannotator protein-tensor
Arguments:
input file for the tensor
threads
Options:
-h, --help Print help
```
```
plot the specific ids information
Usage: toxannotator extract-seq
Arguments:
file to the annotation
idsfile
threads
Options:
-h, --help Print help
toxannotator extract-seq ./testfiles/a1.gff ./testfiles/id.test 4
```
```
compare mRNA annotations
Usage: toxannotator comparem-rna
Arguments:
path to the first gff
path to the second gff
threads
Options:
-h, --help Print help
```
```
compare fasta and gff for the same and different ids and sequences
Usage: toxannotator compare-fasta-gff
Arguments:
path to the first gff
path to the second gff
path to the first fasta
path to the second fasta
threads
Options:
-h, --help Print help
```
- To install windows version:
```
rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/ensemblcov.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc
Gaurav Sablok \
codeprog@icloud.com