{"id":25977637,"url":"https://github.com/nylander/efasta2fasta","last_synced_at":"2025-06-27T13:38:32.280Z","repository":{"id":146538542,"uuid":"46116024","full_name":"nylander/efasta2fasta","owner":"nylander","description":"Convert extended fasta (efasta) to fasta","archived":false,"fork":false,"pushed_at":"2016-02-22T09:26:26.000Z","size":2,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-02T04:15:13.039Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nylander.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-11-13T10:38:02.000Z","updated_at":"2017-05-23T13:45:49.000Z","dependencies_parsed_at":"2023-05-06T09:16:51.616Z","dependency_job_id":null,"html_url":"https://github.com/nylander/efasta2fasta","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/nylander/efasta2fasta","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fefasta2fasta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fefasta2fasta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fefasta2fasta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fefasta2fasta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nylander","download_url":"https://codeload.github.com/nylander/efasta2fasta/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nylander%2Fefasta2fasta/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262266711,"owners_count":23284747,"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":[],"created_at":"2025-03-05T04:38:47.623Z","updated_at":"2025-06-27T13:38:32.255Z","avatar_url":"https://github.com/nylander.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# efasta2fasta\nConvert extended fasta (efasta) to fasta\n\n## The one-liner:\n\n    perl -0076 -ne 'chomp;($h,@r)=split/\\n/;$s=join(\"\",@r);$s=~s/{([\\s|\\w]*),[^}]*}/$1/g;$s=~s/(.{60})/$1\\n/g;print\"\u003e$h\\n$s\\n\" unless(!$h);' file.efasta\n\n#### USAGE\n\n    ./efasta2fasta.pl file.efasta \n\n#### DESCRIPTION\n\nConvert efasta to fasta by taking the first item in the list {,,,} for every ambiguity.\n\n**efasta** - extended fasta format (from [Allpath-LG](http://broadinstitute.org/crd/computational-research-and-development)):\n\n\"ALLPATHS-LG introduces efasta output format, which extends fasta\nformat to capture ambiguities within the assembly which might\notherwise be lost.  These ambiguities may arise from biological\nsources (e.g., SNPs \u0026 CNVs) or from uncertainties in the data.  In\nefasta format, ambiguities are represented as a comma-separated list\nof alternatives within curly braces (\"{}\").  For example, an A/T SNP\nwould become: ATGTC{A,T}TGTCG.  An unresolved homopolymer run where\nthe evidence suggested there should be 6, 7, or 8 Ts would become:\nGTCACTTTTTT{,T,TT}.  Within the braces, alternatives are ordered in\nterms of decreasing likelihood.\"\n\n##### Input:\nefasta file(s)\n\n##### Output:\nfasta file named from the input (with added file ending `.fas`)\n\n#### AUTHOR\n\nJohan Nylander (JN), Johan.Nylander@bils.se\n\n##### COMPANY\n\nBILS/NRM\n\n##### VERSION\n\n1.0\n\n#### CREATED\n\n09/22/2015 02:53:00 PM\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fefasta2fasta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnylander%2Fefasta2fasta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnylander%2Fefasta2fasta/lists"}