{"id":23057375,"url":"https://github.com/applicativesystem/go-diamond-sequence-hints","last_synced_at":"2025-04-03T06:12:42.916Z","repository":{"id":262142601,"uuid":"869102198","full_name":"applicativesystem/go-diamond-sequence-hints","owner":"applicativesystem","description":"extracting the aligned portions from the diamond aligner by read alignment of pacbio reads to the proteins.","archived":false,"fork":false,"pushed_at":"2024-10-16T05:35:58.000Z","size":2965,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-12-16T02:12:08.791Z","etag":null,"topics":["bioinformatics","bioinformatics-data","genome-analysis","genome-annotation","genomealignment","genomeannotation"],"latest_commit_sha":null,"homepage":"","language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/applicativesystem.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-07T18:09:32.000Z","updated_at":"2024-10-16T05:36:02.000Z","dependencies_parsed_at":"2024-11-10T20:18:22.524Z","dependency_job_id":"2359bce8-723f-4a64-ad47-62d45c1ba11d","html_url":"https://github.com/applicativesystem/go-diamond-sequence-hints","commit_stats":null,"previous_names":["applicativesystem/go-diamond-sequence-hints"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-sequence-hints","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-sequence-hints/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-sequence-hints/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/applicativesystem%2Fgo-diamond-sequence-hints/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/applicativesystem","download_url":"https://codeload.github.com/applicativesystem/go-diamond-sequence-hints/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":237863997,"owners_count":19378257,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bioinformatics-data","genome-analysis","genome-annotation","genomealignment","genomeannotation"],"created_at":"2024-12-16T02:12:06.243Z","updated_at":"2025-02-08T19:45:00.840Z","avatar_url":"https://github.com/applicativesystem.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"# go-diamond-sequence-hints\n\n\n- a annotation to sequence extractor for passing the asligned regions as hints. \n- convert your reference aligned sequence fasta to the linearize form \n- 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. \n- this is included in the go-mapper-diamond but if you have the reads to protein alignments then you can use it separately. \n```\nawk '/^\u003e/ {printf(\"\\n%s\\n\",$0);next; } { printf(\"%s\",$0);}  \\\n                         END {printf(\"\\n\");}' inputfasta \u003e output.fasta\n```\n\n```\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \\\ngo run main.go -h\nAnalyzer for the diamond aligner and pacbio reads for hints\n\nUsage:\n  get [command]\n\nAvailable Commands:\n  UpStream\n  alignment\n  completion  Generate the autocompletion script for the specified shell\n  help        Help about any command\n\nFlags:\n  -h, --help   help for get\n\nUse \"get [command] --help\" for more information about a command.\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \\\ngo run main.go alignment -h\nAnalyzes the hsp from the diamond read to protein alignment\n\nUsage:\n  get alignment annotator [flags]\n\nFlags:\n  -a, --alignmentfile string    alignment (default \"alignment file to be analyzed\")\n  -h, --help                    help for alignment\n  -p, --referencefasta string   pacbio file (default \"pacbio reads file\")\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \\\ngo run main.go Upstream -h\nspecific for the genome alignment regions upstream and the downstream of the alignments\n\nUsage:\n  get Upstream Aligner [flags]\n\nFlags:\n  -a, --alignmentfile string             alignment (default \"alignment file to be analyzed\")\n  -d, --downstream of the hsp tags int   downstream tags (default 5)\n  -h, --help                             help for Upstream\n  -p, --referencefasta string            pacbio file (default \"pacbio reads file\")\n  -u, --upstream of the hsp tags int     upstream tags (default 4)\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \\\ngo run main.go UpStream -a matches.tsv -p pacbioreads.fasta -u 10 -d 10                            1 ↵\ngauavsablok@gauravsablok ~/Desktop/codecreatede/golang/go-diamond-sequence-hints ±main⚡ » \\\nls -la\ntotal 88\ndrwxr-xr-x. 1 gauavsablok gauavsablok   256 Oct  8 11:33 .\ndrwxr-xr-x. 1 gauavsablok gauavsablok  1670 Oct  7 21:05 ..\ndrwxr-xr-x. 1 gauavsablok gauavsablok   148 Oct  8 08:00 .git\n-rw-r--r--. 1 gauavsablok gauavsablok   211 Oct  7 23:51 go.mod\n-rw-r--r--. 1 gauavsablok gauavsablok   896 Oct  7 23:51 go.sum\n-rw-r--r--. 1 gauavsablok gauavsablok  5810 Oct  8 11:33 main.go\n-rwxr-xr-x. 1 gauavsablok gauavsablok   324 Oct  8 11:08 matches.tsv\n-rw-r--r--. 1 gauavsablok gauavsablok 54117 Oct  7 20:59 pacbioreads.fasta\n-rw-r--r--. 1 gauavsablok gauavsablok   624 Oct  8 00:04 README.md\n-rw-r--r--. 1 gauavsablok gauavsablok   304 Oct  8 11:32 sequences-annotation.txt\n-rw-r--r--. 1 gauavsablok gauavsablok   384 Oct  8 11:33 sequences-annotation-upstream-downstream.txt\n\n```\n\nGaurav Sablok\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-diamond-sequence-hints","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fapplicativesystem%2Fgo-diamond-sequence-hints","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fapplicativesystem%2Fgo-diamond-sequence-hints/lists"}