Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/applicativesystem/go-goannotate
golang annotation for genome annotation.
https://github.com/applicativesystem/go-goannotate
bioinformatics genestructure genome-analysis genome-annotation genome-annotation-analyzer gff gff3-format gff3-tools golang golang-package graphics-package
Last synced: 19 days ago
JSON representation
golang annotation for genome annotation.
- Host: GitHub
- URL: https://github.com/applicativesystem/go-goannotate
- Owner: applicativesystem
- Created: 2024-09-12T07:26:00.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2024-11-01T18:42:50.000Z (2 months ago)
- Last Synced: 2024-11-10T20:18:09.247Z (about 2 months ago)
- Topics: bioinformatics, genestructure, genome-analysis, genome-annotation, genome-annotation-analyzer, gff, gff3-format, gff3-tools, golang, golang-package, graphics-package
- Language: Go
- Homepage:
- Size: 13.4 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# go-goannotate
- annotation and genome annotation summarizer.
- takes a gff file and summarizes all the regions such as mRNA, cds, protein five prime UTR, and three prime UTR.
- process as many genomes at a single time
```
git clone htts.github.com/go-goannotate
go run main.go
```
- detail usage
```
╰─$ go run main.go -h
annotate and visualize your genome
Usage:
golanannotate [flags]
Flags:
-A, --annotationfile string genome annotation (default "path to the annotation file")
-h, --help help for golanannotate
exit status 1
```
- it will generate the summary
```
╭─gauavsablok@gauravsablok ~/Desktop/go/go-goannotate ‹main●›
╰─$ go run main.go -A sample-file/sample-TAIR10_GFF3_genes.gff
The assembled genome from the gff annotations summare are given below:
The total assembled mRNA are: 26857
The total assembled mRNA plus strand are: 18053
The total assembled mRNA minus strand are: 8804
The total assembled exon are: 19536
The total assembled exon plus strand are: 13976
The total assembled exon minus strand are: 5560
The total assembled cds are: 15712
The total assembled cds plus strand are: 552
The total assembled cds minus strand are: 276
The total assembled protein are: 22456
The total assembled protein plus strand are: 16990
The total assembled protein minus strand are: 5466
The total assembled five are: 1477
The total assembled five plus strand are: 602
The total assembled five minus strand are: 875
The total assembled three are: 2128
The total assembled three plus strand are: 455
The total assembled three minus strand are: 1673
exit status 1
```
Gaurav Sablok