- a dimaond mapping of the pacbiohifi reads/fasta to the protein databases.
- It just needs the pacbiohifi reads and the protein database and it aligns them and extracts the regions and store them as structs and interfaces.
- diamond mapper can be found at diamond mapper
- for hint generation and tag generation for AUGUSTUS and BRAKER and the sequence extraction for generating the environmental tags for the sequencing.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go -h
This is golang application for generating the hints from the protein alignment to pacbiohifi reads
Usage:
flag [command]
Available Commands:
align
completion Generate the autocompletion script for the specified shell
help Help about any command
hspalignment
pacbio
proteinalignment
seqHsp
upStreamHSP
Flags:
-h, --help help for flag
Use "flag [command] --help" for more information about a command.
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go align -h
this option aligns and analyze all together and it requires only the proteins and the reference pacbio or the other fasta file
Usage:
flag align and analyze [flags]
Flags:
-h, --help help for align
-p, --pacbio string read-protein alignment (default "reads for protein alignment")
-f, --pacbiofolder string pacbio conversion (default "folder containing the bam files and the pbi files")
-P, --protein string protein datasets for the alignment (default "protein datasets")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go hspalignment -h
Analyzes the hsp from the diamond read to protein alignment
Usage:
flag hspalignment [flags]
Flags:
-a, --alignmentfile string alignment (default "alignment file to be analyzed")
-h, --help help for hspalignment
-p, --referencefasta string pacbio file (default "pacbio reads file")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go pacbio -h
converts the pacbio reads to the fasta format for the alignment and annotations, provide the folder path
Usage:
flag pacbio [flags]
Flags:
-h, --help help for pacbio
-f, --pacbiofolder string pacbio conversion (default "folder containing the bam files and the pbi files")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go proteinalignment -h
aligns the pacbio reads or the fasta reads to the proteins
Usage:
flag proteinalignment [flags]
Flags:
-h, --help help for proteinalignment
-p, --pacbio string read-protein alignment (default "reads for protein alignment")
-P, --protein string protein datasets for the alignment (default "protein datasets")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go seqHsp -h
Analyzes the hsp from the diamond read to protein alignment
Usage:
flag seqHsp [flags]
Flags:
-a, --alignmentfile string alignment (default "alignment file to be analyzed")
-h, --help help for seqHsp
-p, --referencefasta string pacbio file (default "pacbio reads file")
gauavsablok@gauravsablok ~/Desktop/codecreatede/golang/gomapper-diamond ±main⚡ » \
go run main.go upStreamHSP -h
specific for the genome alignment regions upstream and the downstream of the alignments
Usage:
flag upStreamHSP [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 upStreamHSP
-p, --referencefasta string pacbio file (default "pacbio reads file")
-u, --upstream of the hsp tags int upstream tags (default 4)
- the usage of the corresponding each section is given below:
go run main.go seqHsp -a ./samplefiles/matches.tsv -p ./samplefiles/fastafile.fasta
go run main.go upStreamHSP -a ./samplefiles/matches.tsv -p ./samplefiles/fastafile.fasta -u 10 -d 10
go run main.go alignment -a matches.tsv -p ./samplefiles/pacbioreads.fasta
go run main.go analyze -a ./samplefiles/matches.tsv -P ./samplefiles/fastafile.fasta
- in case of the binary use the following should be done
./gomapperdiamod -h
./gomapperdiamond seqHsp -a ./samplefiles/matches.tsv -p ./samplefiles/fastafile.fasta
./gomappeddiamond upStreamHSP -a ./samplefiles/matches.tsv -p ./samplefiles/fastafile.fasta -u 10 -d 10
./gomapperdiamond alignment -a matches.tsv -p ./samplefiles/pacbioreads.fasta
./gomapperdiamond analyze -a ./samplefiles/matches.tsv -P ./samplefiles/fastafile.fasta
Gaurav Sablok