{"id":23505673,"url":"https://github.com/gamcil/frippa","last_synced_at":"2025-06-12T18:07:03.927Z","repository":{"id":113168319,"uuid":"210772513","full_name":"gamcil/frippa","owner":"gamcil","description":"Fungal Ribosimally synthesized and Post-translationally modified Peptide (RiPP) assayer","archived":false,"fork":false,"pushed_at":"2021-12-14T04:31:16.000Z","size":160,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-06-12T18:05:52.837Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/gamcil.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":"2019-09-25T06:33:51.000Z","updated_at":"2021-12-14T04:31:19.000Z","dependencies_parsed_at":"2023-03-13T13:22:56.392Z","dependency_job_id":null,"html_url":"https://github.com/gamcil/frippa","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/gamcil/frippa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2Ffrippa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2Ffrippa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2Ffrippa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2Ffrippa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gamcil","download_url":"https://codeload.github.com/gamcil/frippa/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gamcil%2Ffrippa/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259518832,"owners_count":22870301,"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":"2024-12-25T09:38:53.881Z","updated_at":"2025-06-12T18:07:03.883Z","avatar_url":"https://github.com/gamcil.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# frippa\nFungal Ribosimally synthesized and Post-translationally modified Peptide (RiPP) assayer\n\n## Installation\nThe quickest way to start using fRiPPa is by using Docker. Note that due to licensing,\nyou have to grab your own copy of SignalP 5.0b first ([here](https://services.healthtech.dtu.dk/software.php)).\n\nFirst, download the [fRiPPa Dockerfile](https://raw.githubusercontent.com/gamcil/frippa/master/Dockerfile)\nand place it in the same directory as your downloaded copy of SignalP. You should have\nthe following files:\n\n```\nDockerfile\nsignalp-5.0b.Linux.tar.gz\n```\n\nThen, you can build a Docker image by:\n\n```\ndocker build -t frippa -f Dockerfile .\n```\n\nOnce you have built the image, the easiest way to use it is by using the [wrapper BASH\nscript](https://raw.githubusercontent.com/gamcil/frippa/master/frippa-docker). For\nexample:\n\n```sh\nwget https://raw.githubusercontent.com/gamcil/frippa/master/frippa-docker\nchmod +x frippa-docker\nfrippa-docker genome.gbk\n```\n\nThis will download the wrapper script, ``frippa-docker``, make it executable, and run\nit on ``genome.gbk``. You can put this script somewhere on your system ``$PATH`` to\naccess it from anywhere.\n\nThe wrapper script will mount the present working directory (``$PWD``; the directory\nyou're in when you launched ``frippa-docker``) as the working directory, allowing you to\npass files between the host system and the docker container. Note: files must be\nsomewhere **inside** the ``$PWD``; using e.g. ``../path/outside/pwd`` will not work.\n\nUnder the hood, this is the equivalent of:\n\n```sh\nWORKDIR=\"${PWD}\"\nMOUNT=\"type=bind,source=${WORKDIR},target=${WORKDIR}\"\n\ndocker run --rm \"${IT[@]}\" \\\n  --workdir \"${WORKDIR}\" \\\n  --mount \"${MOUNT}\" \\\n  frippa \\\n  frippa genome.gbk\n```\n\n## Usage\n```\nusage: frippa [-h] [-o OUTPUT] [-t THREADS] [-e EVALUE] [-n NEIGHBOURS]\n              [-v OVERLAP] [-ra] [-cp CUTSITE_PCT] [-mr MIN_REPEATS]\n              [-min_rl MIN_REPEAT_LENGTH] [-max_rl MAX_REPEAT_LENGTH]\n              [-rs REPEAT_SIMILARITY] [-zc Z_SCORE_CUTOFF]\n              genbank\n\npositional arguments:\n  genbank               Input GenBank file\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -o OUTPUT, --output OUTPUT\n                        Path to write results to\n  -t THREADS, --threads THREADS\n                        How many threads to use when running hmmsearch and\n                        SignalP\n  -e EVALUE, --evalue EVALUE\n                        E-value cutoff to use when filtering hmmsearch results\n\nCluster prediction settings:\n  -n NEIGHBOURS, --neighbours NEIGHBOURS\n                        Number of base pair either side of a DUF3328 hit to\n                        grab proteins\n  -v OVERLAP, --overlap OVERLAP\n                        Maximum percentage of overlapping proteins before\n                        clusters are merged\n  -ra, --report_all     Report all clusters with DUF3328 hits, even if no\n                        repeat predictions\n\nRepeat filtering:\n  -cp CUTSITE_PCT, --cutsite_pct CUTSITE_PCT\n                        Threshold for total cut sites in individual repeats\n  -mr MIN_REPEATS, --min_repeats MIN_REPEATS\n                        Minimum number of detected repeats\n  -min_rl MIN_REPEAT_LENGTH, --min_repeat_length MIN_REPEAT_LENGTH\n                        Minimum length of a repeat sequence.\n  -max_rl MAX_REPEAT_LENGTH, --max_repeat_length MAX_REPEAT_LENGTH\n                        Maximum length of a repeat sequence. Long sequences\n                        tend to be red herrings\n  -rs REPEAT_SIMILARITY, --repeat_similarity REPEAT_SIMILARITY\n                        Average (hamming) similarity threshold for repeat\n                        sequences\n  -zc Z_SCORE_CUTOFF, --z_score_cutoff Z_SCORE_CUTOFF\n                        Minimum z-score for a repeat sequence\n```\n\nNote that you will have to provid\n\n## Dependencies\nfRiPPa requires all following tools to be available on the system $PATH:\n\n### lfasta from the FASTA2 package\n\n```\nmkdir fasta2\ncd fasta2\nwget http://faculty.virginia.edu/wrpearson/fasta/fasta2/fasta2.shar.Z\ngunzip fasta2.shar.Z\nsh fasta2.shar\nmake lfasta\n```\n\n### RADAR\n\nDownload latest release from GitHub (https://github.com/AndreasHeger/radar/releases)\n\n```\ntar -xvzf radar-x.x.x.tgz\ncd radar-x.x.x.tgz\n./configure\nmake; make install\n```\n\n### SignalP 5.0\n\nObtain executable from: https://services.healthtech.dtu.dk/software.php\n\n### hmmsearch from HMMER\n\nObtain from: http://hmmer.org/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgamcil%2Ffrippa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgamcil%2Ffrippa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgamcil%2Ffrippa/lists"}