{"id":25977582,"url":"https://github.com/nylander/degap_fasta_alignment","last_synced_at":"2025-07-28T19:10:16.770Z","repository":{"id":279455080,"uuid":"938873030","full_name":"nylander/degap_fasta_alignment","owner":"nylander","description":"Remove columns in large fasta formatted alignments containing all-missing data.","archived":false,"fork":false,"pushed_at":"2025-03-31T15:48:12.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-31T17:01:06.562Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","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/nylander.png","metadata":{"files":{"readme":"README.md","changelog":"ChangeLog","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":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-02-25T16:28:10.000Z","updated_at":"2025-03-31T15:48:16.000Z","dependencies_parsed_at":"2025-02-25T17:34:33.276Z","dependency_job_id":"c459c6f6-2e07-43a2-9077-e0f292aa7874","html_url":"https://github.com/nylander/degap_fasta_alignment","commit_stats":null,"previous_names":["nylander/degap_fasta_alignment"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nylander/degap_fasta_alignment","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fdegap_fasta_alignment","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fdegap_fasta_alignment/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fdegap_fasta_alignment/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fdegap_fasta_alignment/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nylander","download_url":"https://codeload.github.com/nylander/degap_fasta_alignment/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fdegap_fasta_alignment/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267570006,"owners_count":24109180,"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","status":"online","status_checked_at":"2025-07-28T02:00:09.689Z","response_time":68,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2025-03-05T04:38:34.382Z","updated_at":"2025-07-28T19:10:16.761Z","avatar_url":"https://github.com/nylander.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DFA - Degap Fasta Alignments\n\n- Last modified: mån mar 31, 2025  05:46\n- Sign: JN\n\n## Description\n\nRemove columns in large fasta-formatted alignments containing all-missing data.\n\nDesigned to make minimal memory footprint.\n\n## Installation\n\nSee [INSTALL](INSTALL)\n\n## Usage\n\n    $ dfa [options] infile(s).\n\n## Options:\n\n- `-h`               show help\n- `-V`               print version\n- `-v`               be verbose\n- `-m missing_chars` characters treated as missing (default: `Nn?Xx-`)\n- `-w wrap_length`   wrap sequences to length `wrap_length` (default: `60`)\n\n`infile` should be in fasta format.\n\n## Examples\n\nInput example ([in.fas](data/in.fas))\n\n    $ cat data/in.fas\n    \u003eApa\n    ANN-C\n    \u003eBpa\n    ANT-C\n\n    $ dfa data/in.fas\n    \u003eApa\n    ANC\n    \u003eBpa\n    ATC\n\n    $ dfa -m - data/in.fas\n    \u003eApa\n    ANNC\n    \u003eBpa\n    ANTC\n\n## Scripts\n\n### [`remove_empty_alignment_columns.py`](scripts/remove_empty_alignment_columns.py)\n\nRemove columns from multiple sequence alignment containing all missing data.\nWritten in python with low memory footprint in mind.\n\nSee output from `remove_empty_alignment_columns.py -h` for usage.\n\n### [`degap_fasta_alignment.pl`](scripts/degap_fasta_alignment.pl)\n\nScript written i perl for removing gaps (missing) characters in fasta\nalignments. The original script is taken from [fastagap\nrepository](https://github.com/nylander/fastagap/blob/main/degap_fasta_alignment.pl).\nThis script have some extra options for removing gaps (missing data).  Note,\nhowever, the script can not handle very large alignments.\n\nSee output from `degap_fasta_alignment.pl -h` for usage.\n\n## License and copyright\n\nCopyright 2025 Johan Nylander\n\n[MIT License](LICENSE)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fdegap_fasta_alignment","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnylander%2Fdegap_fasta_alignment","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fdegap_fasta_alignment/lists"}