{"id":21882278,"url":"https://github.com/bfssi-bioinformatics-lab/seqpresenceabsence","last_synced_at":"2025-03-22T01:14:59.153Z","repository":{"id":33433763,"uuid":"158400778","full_name":"BFSSI-Bioinformatics-Lab/SeqPresenceAbsence","owner":"BFSSI-Bioinformatics-Lab","description":"Package for checking for the presence/absence of markers against a set of samples","archived":false,"fork":false,"pushed_at":"2022-12-08T01:18:21.000Z","size":71,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-26T19:14:05.667Z","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/BFSSI-Bioinformatics-Lab.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}},"created_at":"2018-11-20T14:18:39.000Z","updated_at":"2019-06-14T15:41:13.000Z","dependencies_parsed_at":"2023-01-15T00:54:03.158Z","dependency_job_id":null,"html_url":"https://github.com/BFSSI-Bioinformatics-Lab/SeqPresenceAbsence","commit_stats":null,"previous_names":["bfssi-forest-dussault/seqpresenceabsence"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2FSeqPresenceAbsence","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2FSeqPresenceAbsence/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2FSeqPresenceAbsence/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BFSSI-Bioinformatics-Lab%2FSeqPresenceAbsence/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BFSSI-Bioinformatics-Lab","download_url":"https://codeload.github.com/BFSSI-Bioinformatics-Lab/SeqPresenceAbsence/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244890097,"owners_count":20527035,"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":"2024-11-28T09:28:08.742Z","updated_at":"2025-03-22T01:14:59.127Z","avatar_url":"https://github.com/BFSSI-Bioinformatics-Lab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# seqPresenceAbsence\n\n### Requirements\n- Python \u003e= 3.6\n- [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs\u0026DOC_TYPE=Download) (makeblastdb and blastn must be in your $PATH)\n- [MUSCLE](https://www.drive5.com/muscle/) (muscle must be in your $PATH)\n\n### Installation\n```\npip install seqPresenceAbsence\n```\n\n### Usage\n```\nUsage: seqPresenceAbsence [OPTIONS]\n\n  seqPresenceAbsence is a simple script for querying an input nucleotide\n  FASTA file against a database of sequences. Will return an .xlsx and .csv\n  report of presence/absence of the sequences. Version: 0.2.0.\n\nOptions:\n  -i, --indir PATH           Path to directory containing FASTA files you want\n                             to query  [required]\n  -t, --targets PATH         Path to multi-FASTA containing targets of\n                             interest  [required]\n  -o, --outdir PATH          Root directory to store all output files\n                             [required]\n  -p, --perc_identity FLOAT  Equivalent to the -perc_identity argument in\n                             blastn. Defaults to 95.00.\n  -k, --keep_db_seqs         Set this flag to keep the target sequence in\n                             addition to the query sequence from BLAST.\n  -v, --verbose              Set this flag to enable more verbose logging.\n  --version                  Specify this flag to print the version and exit.\n  --help                     Show this message and exit.\n```\n\n### References\n- Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput\n  Nucleic Acids Res. 32(5):1792-1797","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbfssi-bioinformatics-lab%2Fseqpresenceabsence","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbfssi-bioinformatics-lab%2Fseqpresenceabsence","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbfssi-bioinformatics-lab%2Fseqpresenceabsence/lists"}