https://github.com/applicativesystem/go-nuc-iter
golang nuc-iteration
https://github.com/applicativesystem/go-nuc-iter
bioinformatics genome-analysis genome-analysis-annotation genome-assembly genome-informatics
Last synced: about 2 months ago
JSON representation
golang nuc-iteration
- Host: GitHub
- URL: https://github.com/applicativesystem/go-nuc-iter
- Owner: applicativesystem
- Created: 2024-10-23T09:55:52.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2024-10-23T20:31:17.000Z (12 months ago)
- Last Synced: 2024-12-16T02:12:08.316Z (10 months ago)
- Topics: bioinformatics, genome-analysis, genome-analysis-annotation, genome-assembly, genome-informatics
- Language: Go
- Homepage:
- Size: 7.06 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# go-nuc-iter
- a go implementation the same speed as the RUST.
- to compare against RUST, a RUSt version with the RUST docker is also present.
- golang has no unique function, so implemented a additional string compare.
```
╭─gauavsablok@gauravsablok ~/Desktop/go/go-nuc-iter ‹main●›
╰─$ go run main.go -h
Finding the origin of the kmer
Usage:
sequence [command]
Available Commands:
completion Generate the autocompletion script for the specified shell
genome
help Help about any command
illumina
pacbio
Flags:
-h, --help help for sequence
Use "sequence [command] --help" for more information about a command.
exit status 1
╭─gauavsablok@gauravsablok ~/Desktop/go/go-nuc-iter ‹main●›
╰─$ go run main.go pacbio -h 1 ↵
Pacbio finding the original kmer
Usage:
sequence pacbio [flags]
Flags:
-h, --help help for pacbio
-A, --kmerArgs int origin kmer (default 10)
-P, --pacbiofile string pacbioinsert (default "pacbiofile to be analyzed")
exit status 1
╭─gauavsablok@gauravsablok ~/Desktop/go/go-nuc-iter ‹main●›
╰─$ go run main.go illumina -h 1 ↵
illumina finding the original kmer
Usage:
sequence illumina [flags]
Flags:
-h, --help help for illumina
-i, --illuminafile string pacbioinsert (default "pacbiofile to be analyzed")
-A, --kmerArgs int origin kmer (default 10)
exit status 1
╭─gauavsablok@gauravsablok ~/Desktop/go/go-nuc-iter ‹main●›
╰─$ go run main.go genome -h 1 ↵
Genome finding the original kmer
Usage:
sequence genome [flags]
Flags:
-G, --genomefile string pacbioinsert (default "pacbiofile to be analyzed")
-h, --help help for genome
-A, --kmerArgs int origin kmer (default 10)
exit status 1
```
- it will produce a SAM compatible format which will give the start, end, kmer, origin of the kmer and all the other details.
- writing a interconvertible which will convert this into a hash Btree.
```
0 5 ATACT ATACTTTAAATTTTAGTTACTATTAT
1 6 TACTT ATACTTTAAATTTTAGTTACTATTAT
2 7 ACTTT ATACTTTAAATTTTAGTTACTATTAT
3 8 CTTTA ATACTTTAAATTTTAGTTACTATTAT
4 9 TTTAA ATACTTTAAATTTTAGTTACTATTAT
```
Gaurav Sablok