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https://github.com/applicativesystem/go-diamond-sequence-hints
extracting the aligned portions from the diamond aligner by read alignment of pacbio reads to the proteins.
https://github.com/applicativesystem/go-diamond-sequence-hints
bioinformatics bioinformatics-data genome-analysis genome-annotation genomealignment genomeannotation
Last synced: 24 days ago
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extracting the aligned portions from the diamond aligner by read alignment of pacbio reads to the proteins.
- Host: GitHub
- URL: https://github.com/applicativesystem/go-diamond-sequence-hints
- Owner: applicativesystem
- License: mit
- Created: 2024-10-07T18:09:32.000Z (3 months ago)
- Default Branch: main
- Last Pushed: 2024-10-16T05:35:58.000Z (3 months ago)
- Last Synced: 2024-11-10T20:18:08.814Z (about 2 months ago)
- Topics: bioinformatics, bioinformatics-data, genome-analysis, genome-annotation, genomealignment, genomeannotation
- Language: Go
- Homepage:
- Size: 2.83 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# go-diamond-sequence-hints
- a annotation to sequence extractor for passing the asligned regions as hints.
- convert your reference aligned sequence fasta to the linearize form
- it extracts and write a fasta so that you can use the aligned regions either for the annotations or simply for generating the tags for the specific regions.
- this is included in the go-mapper-diamond but if you have the reads to protein alignments then you can use it separately.
```
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} \
END {printf("\n");}' inputfasta > output.fasta
```
```
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \
go run main.go -h
Analyzer for the diamond aligner and pacbio reads for hints
Usage:
get [command]
Available Commands:
UpStream
alignment
completion Generate the autocompletion script for the specified shell
help Help about any command
Flags:
-h, --help help for get
Use "get [command] --help" for more information about a command.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \
go run main.go alignment -h
Analyzes the hsp from the diamond read to protein alignment
Usage:
get alignment annotator [flags]
Flags:
-a, --alignmentfile string alignment (default "alignment file to be analyzed")
-h, --help help for alignment
-p, --referencefasta string pacbio file (default "pacbio reads file")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \
go run main.go Upstream -h
specific for the genome alignment regions upstream and the downstream of the alignments
Usage:
get Upstream Aligner [flags]
Flags:
-a, --alignmentfile string alignment (default "alignment file to be analyzed")
-d, --downstream of the hsp tags int downstream tags (default 5)
-h, --help help for Upstream
-p, --referencefasta string pacbio file (default "pacbio reads file")
-u, --upstream of the hsp tags int upstream tags (default 4)
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \
go run main.go UpStream -a matches.tsv -p pacbioreads.fasta -u 10 -d 10 1 ↵
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \
ls -la
total 88
drwxr-xr-x. 1 gauavsablok gauavsablok 256 Oct 8 11:33 .
drwxr-xr-x. 1 gauavsablok gauavsablok 1670 Oct 7 21:05 ..
drwxr-xr-x. 1 gauavsablok gauavsablok 148 Oct 8 08:00 .git
-rw-r--r--. 1 gauavsablok gauavsablok 211 Oct 7 23:51 go.mod
-rw-r--r--. 1 gauavsablok gauavsablok 896 Oct 7 23:51 go.sum
-rw-r--r--. 1 gauavsablok gauavsablok 5810 Oct 8 11:33 main.go
-rwxr-xr-x. 1 gauavsablok gauavsablok 324 Oct 8 11:08 matches.tsv
-rw-r--r--. 1 gauavsablok gauavsablok 54117 Oct 7 20:59 pacbioreads.fasta
-rw-r--r--. 1 gauavsablok gauavsablok 624 Oct 8 00:04 README.md
-rw-r--r--. 1 gauavsablok gauavsablok 304 Oct 8 11:32 sequences-annotation.txt
-rw-r--r--. 1 gauavsablok gauavsablok 384 Oct 8 11:33 sequences-annotation-upstream-downstream.txt
```
Gaurav Sablok