{"id":15704351,"url":"https://github.com/poisonalien/gtf2fasta","last_synced_at":"2025-04-30T10:49:05.155Z","repository":{"id":182576278,"uuid":"88495004","full_name":"PoisonAlien/gtf2fasta","owner":"PoisonAlien","description":"Tookit for gtf format conversion and sequence extraction","archived":false,"fork":false,"pushed_at":"2024-01-26T14:55:06.000Z","size":11,"stargazers_count":5,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-30T10:49:02.958Z","etag":null,"topics":["gtf","rna-seq"],"latest_commit_sha":null,"homepage":null,"language":"Julia","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/PoisonAlien.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":"2017-04-17T09:52:04.000Z","updated_at":"2024-01-26T14:55:35.000Z","dependencies_parsed_at":"2024-10-24T08:15:56.617Z","dependency_job_id":null,"html_url":"https://github.com/PoisonAlien/gtf2fasta","commit_stats":{"total_commits":9,"total_committers":2,"mean_commits":4.5,"dds":"0.11111111111111116","last_synced_commit":"ae1407e842d9d59661b01b4212001f6f44bccaa9"},"previous_names":["poisonalien/gtfsanta"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fgtf2fasta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fgtf2fasta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fgtf2fasta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PoisonAlien%2Fgtf2fasta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PoisonAlien","download_url":"https://codeload.github.com/PoisonAlien/gtf2fasta/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251685131,"owners_count":21627242,"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":["gtf","rna-seq"],"created_at":"2024-10-03T20:11:31.158Z","updated_at":"2025-04-30T10:49:05.098Z","avatar_url":"https://github.com/PoisonAlien.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# gtf2fasta\nA minimal tool for sequence extraction for every transcript (only from exonic regions) in a [gtf](http://mblab.wustl.edu/GTF22.html) from a fasta file. \n\nIt's written in [Julia](https://julialang.org/) and has no dependencies. See [here](https://julialang.org/downloads/) for Julia installation.\n\nThis tool requires [indexed fasta file](http://www.htslib.org/doc/faidx.html) for memory efficient sequence extraction.\n\n## Usage\n\n```bash\n#Extracting fasta sequence from gtf file (sequences are written to stdout)\n\n$ gtf2fasta.jl ens82.gtf hg19.fa | head\n\u003eENST00000456328\nGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCA\nGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCA\nGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTG\n...\n```\n\nIt will also generate `ens82.gtf.transcript.dict.tsv` with transcript to gene mappings.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fgtf2fasta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpoisonalien%2Fgtf2fasta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpoisonalien%2Fgtf2fasta/lists"}