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https://github.com/applicativesystem/go-alignment-block-estimate
estimate blocks alignment stats
https://github.com/applicativesystem/go-alignment-block-estimate
bioinformatics bioinformatics-tool genome-alignment genome-alignment-bioinformatics genome-analysis golang-package phylogenomics phylogenomics-bioinformatics
Last synced: 16 days ago
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estimate blocks alignment stats
- Host: GitHub
- URL: https://github.com/applicativesystem/go-alignment-block-estimate
- Owner: applicativesystem
- License: mit
- Created: 2024-09-22T07:21:41.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2024-09-29T07:47:24.000Z (3 months ago)
- Last Synced: 2024-11-10T20:18:10.288Z (about 2 months ago)
- Topics: bioinformatics, bioinformatics-tool, genome-alignment, genome-alignment-bioinformatics, genome-analysis, golang-package, phylogenomics, phylogenomics-bioinformatics
- Language: Go
- Homepage:
- Size: 8.79 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# go-alignment-block-estimate
- a alignment block estimates of the selected block.
- define the start and the stop of the alignment regions and it computes all the stats from the given block region
- it will only process that block of the alignment and not the complete alignment.
```
[gauravsablok@ultramarine]~/Desktop/codecreatede/go-alignment-block-estimate% \
go run main.go -h
This estimates the site proportion in your whole genome or gene specific alignment
Usage:
flags [flags]
Flags:
-a, --alignmentfile string a alignment file (default "align")
-e, --endcoordinate int end of the alignment block (default 40)
-h, --help help for flags
-s, --startcoordinate int start of the alignment block (default 1)
[gauravsablok@ultramarine]~/Desktop/codecreatede/go-alignment-block-estimate% \
go run main.go -a ./samplefile/samplealignment.fasta -s 1 -e 10
The collinearity block for A as a base pattern and T as a mismatch is 1
The collinearity block for A as a base pattern G as a mismatch is 1
The collinearity block for A as a base pattern and C as a mismatch is 0
The collinearity block for T as a base pattern and G as a mismatch is 0
The collinearity block for T as a base pattern C as a mismatch is %d 0
The collinearity block for T as a base pattern and A as a mismatch is 0
The collinearity block for G as a base pattern and C as a mismatch is 0
The collinearity block for G as a base pattern A as a mismatch is 0
The collinearity block for G as a base pattern and T as a mismatch is 0
The collinearity block for C as a base pattern and A as a mismatch is 0
The collinearity block for C as a base pattern T as a mismatch is %d 0
The collinearity block for C as a base pattern and G as a mismatch is 0
The number of the unified bases across A are 0
The number of the unified bases across T are 0
The number of the unified bases across G are 0
The number of the unified bases across C are 1
```
Gaurav Sablok