{"id":33922451,"url":"https://github.com/rustcodepro/toxannotator","last_synced_at":"2026-01-13T14:01:09.861Z","repository":{"id":326964581,"uuid":"1106213166","full_name":"rustcodepro/toxannotator","owner":"rustcodepro","description":"rustic tox annotator for comparative 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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","deep-learning","deep-neural-networks","genome-annotation","toxgenomics"],"created_at":"2025-12-12T09:02:53.404Z","updated_at":"2026-01-13T14:01:09.815Z","avatar_url":"https://github.com/rustcodepro.png","language":"Rust","readme":"# toxannotator\n\n- a toxdb annotator for genomic comparison for comparative genomics. \n- ready to use tables for comparative analysis. \n- genomic comparison and annotation plotters. \n\n```\ncargo build\n```\n\n```\n_____                                                  _             _                  \n|_   _|   ___   __  __   __ _   _ __    _ __     ___   | |_    __ _  | |_    ___    _ __ \n | |    / _ \\  \\ \\/ /  / _` | | '_ \\  | '_ \\   / _ \\  | __|  / _` | | __|  / _ \\  | '__|\n | |   | (_) |  \u003e  \u003c  | (_| | | | | | | | | | | (_) | | |_  | (_| | | |_  | (_) | | |   \n |_|    \\___/  /_/\\_\\  \\__,_| |_| |_| |_| |_|  \\___/   \\__|  \\__,_|  \\__|  \\___/  |_|   \n                                                                                        \n\nA toxodb annotator.\n     ************************************************\n     Gaurav Sablok,\n     Email: codeprog@icloud.com\n    ************************************************\n\nUsage: toxannotator \u003cCOMMAND\u003e\n\nCommands:\nprotein-compare              Only compare protein coding\nprotein-compare-seq-command  Compare protein coding coordinates and sequences also\nprotein-plotter              Plot the protein coding regions\nprotein-tensor               Prepare the protein tensor for the machine and deep learning\nextract-seq                  plot the specific ids information\ncomparem-rna                 compare mRNA annotations\ncompare-fasta-gff            compare fasta and gff for the same and different ids and sequences\nhelp                         Print this message or the help of the given subcommand(s)\n\nOptions:\n-h, --help     Print help\n-V, --version  Print version\n\n\n```\n\n```\nOnly compare protein coding\n\nUsage: toxannotator protein-compare \u003cGFFFILE1\u003e \u003cGFFFILE2\u003e\n\nArguments:\n  \u003cGFFFILE1\u003e  path to the first gff file\n  \u003cGFFFILE2\u003e  path to the second gff file\n\nOptions:\n  -h, --help  Print help\n  \ntoxannotator protein-compare ./testfiles/a1.gff ./testfiles/b1.gff  4\n\ncommonggenes-same-strand.txt\nTGME49_200010\tTGME49_200010\t2245476\t2245476\t2249210\t2248187\t-\t-\n\nGeneName\tStart1\tStart2\tEnd1\tEnd2\tStrand1\tStrand2\tStart Difference\tEnd Difference\nTGME49_200010\t2245476\t2245476\t2249210\t2248187\t-\t-\t0\t1023\n\n```\n\n```\n\nCompare protein coding coordinates and sequences also\n\nUsage: toxannotator protein-compare-seq-command \u003cGFFFILE1\u003e \u003cGFFFILE2\u003e \u003cFASTAFILE_1\u003e \u003cFASTAFILE_2\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cGFFFILE1\u003e     path to the first gff file\n  \u003cGFFFILE2\u003e     path to the second gff file\n  \u003cFASTAFILE_1\u003e  fasta1 file\n  \u003cFASTAFILE_2\u003e  fasta2 file\n  \u003cTHREADS\u003e      threads\n\nOptions:\n  -h, --help  Print help\n```\n\n```\nPlot the protein coding regions\n\nUsage: toxannotator protein-plotter \u003cINPUTFILE1\u003e \u003cINPUTFILE2\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cINPUTFILE1\u003e  input file 1\n  \u003cINPUTFILE2\u003e  input file 2\n  \u003cTHREADS\u003e     threads\n\nOptions:\n  -h, --help  Print help\n  \ntoxannotator protein-plotter ./testfiles/a1.gff ./testfiles/b1.gff 4\n```\n\n```\nPrepare the protein tensor for the machine and deep learning\n\nUsage: toxannotator protein-tensor \u003cINPUTFILE\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cINPUTFILE\u003e  input file for the tensor\n  \u003cTHREADS\u003e    threads\n\nOptions:\n  -h, --help  Print help\n\n```\n\n```\nplot the specific ids information\n\nUsage: toxannotator extract-seq \u003cANNOTATIONFILE\u003e \u003cIDSFILE\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cANNOTATIONFILE\u003e  file to the annotation\n  \u003cIDSFILE\u003e         idsfile\n  \u003cTHREADS\u003e         threads\n\nOptions:\n  -h, --help  Print help\n  \ntoxannotator extract-seq ./testfiles/a1.gff ./testfiles/id.test 4\n```\n\n```\ncompare mRNA annotations\n\nUsage: toxannotator comparem-rna \u003cGFF_1\u003e \u003cGFF_2\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cGFF_1\u003e    path to the first gff\n  \u003cGFF_2\u003e    path to the second gff\n  \u003cTHREADS\u003e  threads\n\nOptions:\n  -h, --help  Print help\n```\n```\ncompare fasta and gff for the same and different ids and sequences\n\nUsage: toxannotator compare-fasta-gff \u003cGFF_1_INPUT\u003e \u003cGFF_2_INPUT\u003e \u003cFASTA_1_INPUT\u003e \u003cFASTA_2_INPUT\u003e \u003cTHREADS\u003e\n\nArguments:\n  \u003cGFF_1_INPUT\u003e    path to the first gff\n  \u003cGFF_2_INPUT\u003e    path to the second gff\n  \u003cFASTA_1_INPUT\u003e  path to the first fasta\n  \u003cFASTA_2_INPUT\u003e  path to the second fasta\n  \u003cTHREADS\u003e        threads\n\nOptions:\n  -h, --help  Print help\n```\n\n- To install windows version:\n\n```\nrustup component add llvm-tools\nrustup target add x86_64-pc-windows-msvc\ngit clone https://github.com/IBCHgenomic/ensemblcov.git\ncd ensemblcov\ncargo xwin build --target x86_64-pc-windows-msvc\n\nGaurav Sablok \\\ncodeprog@icloud.com\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Ftoxannotator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frustcodepro%2Ftoxannotator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Ftoxannotator/lists"}