{"id":18260401,"url":"https://github.com/carrascomj/gowsh","last_synced_at":"2025-08-25T12:22:09.954Z","repository":{"id":105856219,"uuid":"167621321","full_name":"carrascomj/gowsh","owner":"carrascomj","description":"Homology searcher of Gene Ontologies based on webscrapping and heuristics.","archived":false,"fork":false,"pushed_at":"2019-02-05T17:27:18.000Z","size":246,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-04-08T23:56:50.460Z","etag":null,"topics":["homology","perl"],"latest_commit_sha":null,"homepage":"","language":"Perl","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/carrascomj.png","metadata":{"files":{"readme":"README.md","changelog":"Changes","contributing":null,"funding":null,"license":"LICENSE.txt","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":"2019-01-25T22:16:10.000Z","updated_at":"2019-02-05T17:25:18.000Z","dependencies_parsed_at":"2023-06-14T13:15:25.597Z","dependency_job_id":null,"html_url":"https://github.com/carrascomj/gowsh","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/carrascomj/gowsh","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Fgowsh","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Fgowsh/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Fgowsh/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Fgowsh/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/carrascomj","download_url":"https://codeload.github.com/carrascomj/gowsh/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/carrascomj%2Fgowsh/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":272063566,"owners_count":24866753,"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","status":"online","status_checked_at":"2025-08-25T02:00:12.092Z","response_time":1107,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["homology","perl"],"created_at":"2024-11-05T10:45:08.998Z","updated_at":"2025-08-25T12:22:09.892Z","avatar_url":"https://github.com/carrascomj.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cp align=\"center\"\u003e\n  \u003cimg src=\"logo.svg\" alt=\"logo\" width=\"400\"/\u003e\n\u003c/p\u003e\n\n# GOWSH\n\nPerl homology searcher based on webscrapping and heuristic approaches. It's supposed to look up in HomoloGene,\nEnsemble and [Inparanoid](http://inparanoid.sbc.su.se/cgi-bin/index.cgi) after running Bidirectional best hit algorithm (BDBH).\n\n## Getting Started\n\nClone the repo on local:\n\n    git clone https://github.com/carrascomj/gowsh\n\nAdd script to path (on your bash initialization file; e.g., ~/bashrc):\n\n    export PATH=$PATH:\"path/to/gowsh/bin\"\n\nThe program requires additional packages that can be installed with [cpanm](https://metacpan.org/pod/cpanm), if not already done:\n\n    cpanm JSON Data::Dumper Bio::SeqIO LWP::Simple File::Basename Getopt::Long XML::Parser\n\nAlternatively, one could install WebAPIsGOWSH as an usual perl package (on 'gowsh/' directory):\n\n    perl Makefile.PL\n    make\n    make install\n\nFinally, formatdb and blast+ are both required.\n\n## Usage\n\ngowsh.pl is the main script. The program takes command-line arguments with\nthe following options:\n\n    gowsh.pl --gfile|go|glist \"path_to_file|GOid|list\" --tfile|torg \"path_to_file|organism\"\n        [--modelf|modelo] \"path_to_file|organism\" --out \"outfile\" --preserve\n\n        --gfile path_to_file: input, genes as multiFASTA\n        --go GOid: input, Genetic Ontology ID (as in AmiGO)\n        --glist list: input, blank separated list gene IDs\n        --tfile path_to_file: multiFASTA containing proteins of genome of target organism\n        --torg organism: target organism name (genus and specie)\n        --modfile path_to_file: optional, multiFASTA containing proteins of genome of model organism\n        --modorg organism: optional, model organism name (genus and specie)\n        --out \"outfile\": optional, name of output file; default \"GOWSH_output.txt\"\n        --preserve: optional, if it's added, (nearly) all files generated will be preserved.\n\n## Running the test\n\nThe script can be tested wit the following command:\n\n    gowsh.pl --go 0048507 --modorg \"arabidopsis thaliana\" --torg \"oryza sativa\"\n\nYou can compare the output with the file \"t/GOWSH_outputq1.tsv\".\n\nThe program will then parse the input file, download both genomes from NCBI and try to match homologues.\n\n## What I Learned\n\nThis code was developed as a project for one subjects of my BSc in Biotechnology (UPM). To sum up, I learned the following concepts:\n* Webscrapping biological information using Perl and [mygene API](http://mygene.info/v3/api#/).\n* Use of Entrez [E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25499/) programmatic access API from NCBI.\n* Use of [Ensembl REST](http://www.ensembl.org/index.html) API.\n* Run BLAST on local using [blast+](https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation).\n* Heuristic algorithms to account for homology.\n* How to build a Perl package.\n* How to write a README.md.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarrascomj%2Fgowsh","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcarrascomj%2Fgowsh","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcarrascomj%2Fgowsh/lists"}