{"id":16271286,"url":"https://github.com/ikergarcia1996/gene2tab","last_synced_at":"2025-04-08T15:29:16.487Z","repository":{"id":207784481,"uuid":"720120078","full_name":"ikergarcia1996/Gene2Tab","owner":"ikergarcia1996","description":"This script is used to convert the output of ABRICATE tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.","archived":false,"fork":false,"pushed_at":"2023-11-18T11:01:07.000Z","size":29,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-20T12:52:39.921Z","etag":null,"topics":["abricate","genomic-data-analysis","genomics","genomics-visualization","table"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/gene2tab","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ikergarcia1996.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":"2023-11-17T16:07:59.000Z","updated_at":"2023-11-18T10:42:55.000Z","dependencies_parsed_at":"2024-11-05T01:42:09.400Z","dependency_job_id":"5adf5dc0-65b2-4740-b077-0975f79d1fa0","html_url":"https://github.com/ikergarcia1996/Gene2Tab","commit_stats":null,"previous_names":["ikergarcia1996/gene2tab"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ikergarcia1996%2FGene2Tab","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ikergarcia1996%2FGene2Tab/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ikergarcia1996%2FGene2Tab/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ikergarcia1996%2FGene2Tab/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ikergarcia1996","download_url":"https://codeload.github.com/ikergarcia1996/Gene2Tab/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247870550,"owners_count":21009875,"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":["abricate","genomic-data-analysis","genomics","genomics-visualization","table"],"created_at":"2024-10-10T18:13:11.155Z","updated_at":"2025-04-08T15:29:16.456Z","avatar_url":"https://github.com/ikergarcia1996.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Gene2Tab\n\n## Description\n\nThis script is used to convert the output of [ABRICATE](https://github.com/tseemann/abricate) tabulated output into a matrix samples with the genes as columns and the presence/absence of the gene as the values.\n\nThe script can use as input a directory containing multiple `.tab` files or a single `.tab` file. The output will be a `.csv` file. Each file should contain the `#File` `Sequence` and `GENE` columns, the other ones are optional. \n\nBy default, **the script will only consider genes with a coverage and identity of 90% or more**. This can be changed with the `--min_coverage` and `--min_identity` flags.\n\nExample: \n    \nFile1.tab\n```tsv\n#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\nIsolate1\tS1-length_513\t53228\t54445\t+\tceoA\t1-1218/1218\t========/======\t2/2\t99.92\t99.67\tcard\tU97042:0-1218\tceoA is a periplasmic linker subunit of the CeoAB-OpcM efflux pump\taminoglycoside;fluoroquinolone\nIsolate1\tS1-length_513\t54491\t57575\t+\tceoB\t1-3084/3084\t========/======\t1/1\t100\t99.87\tcard\tU97042:1263-4347\tceoB is a cytoplasmic membrane component of the CeoAB-OpcM efflux pump\taminoglycoside;fluoroquinolone\nIsolate1\tS1-length_513\t57702\t59240\t+\topcM\t1-1536/1536\t========/======\t5/5\t99.93\t99.16\tcard\tU38944.1:0-1536\tOpcM is an outer membrane factor protein found in Burkholderia cepacia. It is part of the CeoAB-OpcM complex.\taminoglycoside;fluoroquinolone\nIsolate1\tS1-length_233\t145199\t146378\t+\tamrA\t24-1200/1200\t========/======\t15/23\t97.25\t80.84\tcard\tBX571965.1:2152165-2150965\tamrA is the efflux pump subunit of the AmrAB-OprM multidrug efflux complex. amrA corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58.\taminoglycoside\nIsolate1\tS1-length_233\t146394\t149503\t+\tamrB\t1-3110/3132\t========/======\t2/2\t99.27\t88.17\tcard\tBX571965.1:2150949-2147817\tamrB is the membrane fusion protein of the AmrAB-OprM multidrug efflux complex.\taminoglycoside\nIsolate1\tS1-length_265\t25329\t26405\t+\tBurkholderia_pseudomallei_Omp38\t1-1122/1122\t========/======\t14/59\t95.37\t80.78\tcard\tAY312416:0-1122\tHeterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem.\tcarbapenem;cephalosporin;cephamycin;monobactam;penam;penem\nIsolate2\tS2-length_512\t25329\t26405\t+\tBurkholderia_pseudomallei_Omp38\t1-1122/1122\t========/======\t14/59\t95.37\t80.78\tcard\tAY312416:0-1122\tHeterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem.\tcarbapenem;cephalosporin;cephamycin;monobactam;penam;penem\n```\n\nFile2.tab\n```tsv\n#FILE\tSEQUENCE\tSTART\tEND\tSTRAND\tGENE\tCOVERAGE\tCOVERAGE_MAP\tGAPS\t%COVERAGE\t%IDENTITY\tDATABASE\tACCESSION\tPRODUCT\tRESISTANCE\nIsolate2\tS2-length_512\t25329\t26405\t+\tBurkholderia_pseudomallei_Omp38\t1-1122/1122\t========/======\t14/59\t95.37\t80.78\tcard\tAY312416:0-1122\tHeterologous expression of Burkholderia pseudomallei Omp38 (BpsOmp38) in Omp-deficient E. coli host cells lowers their permeability and in consequence their antimicrobial susceptibility to penicillin G cefoxitin ceftazidime and imipenem.\tcarbapenem;cephalosporin;cephamycin;monobactam;penam;penem\n```\n\nWill be converted to:\n\n```csv\nSample,ceoA,ceoB,opcM,amrA,amrB,Burkholderia_pseudomallei_Omp38\nBUR-BAB-IMI-102146,1,1,1,1,1,1\nAA2,0,0,0,0,0,1\n```\n\nIf the `--transpose` flag is used, the output will be:\n\n```csv\nSample,Isolate1,Isolate2\nceoA,1,0\nceoB,1,0\nopcM,1,0\namrA,1,0\namrB,1,0\nBurkholderia_pseudomallei_Omp38,1,1\n```\n\n## Installation\n\n```bash\npip install gene2tab\n```\n\n## Usage\n\nSee all the available options with:\n\n```bash\ngene2tab -h\n```\n\nRunning the script. The input can be a single `.tab` file or a directory containing multiple `.tab` files. The output will be a `.csv` file.\n\n```bash\ngene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 \n```\n\nYou can also transpose the output with the `--transpose` flag.\n\n```bash\ngene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --transpose\n```\n\nIf your files use a different delimiter than tab, you can specify it with the `--input_file_delimiter` flag.\n\n```bash\ngene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --input_file_delimiter ','\n```\n\nIf you want a different delimiter in the output file, you can specify it with the `--output_file_delimiter` flag.\n\n```bash\ngene2tab -i [output_directory or file.tab] -o output.csv --min_coverage 0.9 --min_identity 0.9 --output_delimiter ';'\n```\n\n\n## License\n\nApache License 2.0\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fikergarcia1996%2Fgene2tab","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fikergarcia1996%2Fgene2tab","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fikergarcia1996%2Fgene2tab/lists"}