{"id":26201904,"url":"https://github.com/dmnfarrell/pathogenie","last_synced_at":"2025-04-15T06:02:29.653Z","repository":{"id":88494518,"uuid":"226188048","full_name":"dmnfarrell/pathogenie","owner":"dmnfarrell","description":"Desktop tool for microbial genome annotation and gene detection","archived":false,"fork":false,"pushed_at":"2021-06-22T12:58:39.000Z","size":31823,"stargazers_count":12,"open_issues_count":3,"forks_count":4,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-28T16:43:31.890Z","etag":null,"topics":["amr","antibiotic-resistance","bioinformatics","genome-annotation","genomics","pyqt5"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dmnfarrell.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES","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}},"created_at":"2019-12-05T20:58:35.000Z","updated_at":"2023-05-01T11:12:06.000Z","dependencies_parsed_at":null,"dependency_job_id":"30c2cb8e-a187-4cac-affb-5732a3a6b8ca","html_url":"https://github.com/dmnfarrell/pathogenie","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fpathogenie","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fpathogenie/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fpathogenie/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fpathogenie/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dmnfarrell","download_url":"https://codeload.github.com/dmnfarrell/pathogenie/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249016621,"owners_count":21198832,"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":["amr","antibiotic-resistance","bioinformatics","genome-annotation","genomics","pyqt5"],"created_at":"2025-03-12T03:24:17.330Z","updated_at":"2025-04-15T06:02:29.636Z","avatar_url":"https://github.com/dmnfarrell.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n# pathogenie\n\n\u003cimg align=\"right\" src=img/logo.png width=180px\u003e\n\nThis is a desktop and command line program for annotating draft bacterial and viral genomes. It may also be used for quickly detecting arbitrary sequences such as antibiotic resistance genes (AMR) proteins in nucleotide sequences. It uses Blast to find hits to known gene sequences from sequence databases. The inputs are fasta files. Annotation is performed in a similar manner to Prokka and first requires an assembled genome if you have sequenced reads. The program is written in Python. Currently it is available as a graphical desktop application. A command line tool will also be added. You can also use it from inside Python scripts.\n\n## Usage\n\nThe graphical application can be launched from the terminal using:\n\n```pathogenie-gui```\n\nFrom the GUI you may load fasta files into a table and then run genome annotation or gene finding with custom databases. This program utilises the sequence databases for gene finding compiled by abricate:\n\n* card\n* resfinder\n* arg-annot\n* resfinder\n* ncbi\n* ecoh\n\nThe GUI layout is shown below:\n\n\u003cimg src=img/screenshot1.png width=480px\u003e\n\n## Using in python\n\nRun an annotation on a fasta file like a set of contigs:\n\n```python\nimport pathogenie\nfeatdf,recs = pathogenie.app.run_annotation(filename, threads=10, kingdom='bacteria')\n#save to genbank\npathogenie.tools.recs_to_genbank(recs, gbfile)\n```\n\n## Installation\n\nAll operating systems with Python (\u003e=3.6 required) installed:\n\n```pip install -e git+https://github.com/dmnfarrell/pathogenie.git#egg=pathogenie```\n\n## Dependencies\n\nYou require ncbi-blast+ tools and clustalw for basic gene finding. The following programs are used for genome annotation:\n\n* prodigal\n* hmmer3\n* aragorn\n\n### Linux\n\nThe pip command should work fine but you can also install the [snap](https://snapcraft.io/pathogenie) using:\n\n```sudo snap install pathogenie```\n\nOr download the AppImage. Download from the latest [release page](https://github.com/dmnfarrell/pathogenie/releases) and run as follows:\n\n```\nchmod +x pathogenie-0.4.0-x86_64.AppImage\n./pathogenie-0.4.0-x86_64.AppImage\n```\n\nThe external binaries can all be installed on Debian/Ubuntu based systems using:\n\n```sudo apt install ncbi-blast+ clustal prodigal aragorn hmmer```\n\nThese are NOT needed if you are using the snap or AppImage.\n\n### Windows\n\nThe external executables will be downloaded for you when you first launch the program.\n\nBlast also requires the Visual Studio 2015 C++ redistributable runtime package: https://www.microsoft.com/en-us/download/details.aspx?id=48145\n\n### OSX\n\n**Not yet tested** but may work if you can install the dependencies. You can probably install them with bioconda.\n\n## Use from python\n\nRun an annotation and save the results:\n\n```python\nimport pathogenie\nfor file in fastafiles:  \n    name = os.path.basename(file)\n    out = name+'.gb'    \n    res,recs = pathogenie.run_annotation(file, threads=10)\n    #save genbank\n    pathogenie.recs_to_genbank(recs, out)\n    #save gff\n    pathogenie.recs_to_gff(recs, name+'.gff')\n```\n\n## Links\n\n* [Prokka](https://github.com/tseemann/prokka)\n* [abricate](https://github.com/tseemann/abricate)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Fpathogenie","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdmnfarrell%2Fpathogenie","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Fpathogenie/lists"}