{"id":15292598,"url":"https://github.com/ssi-dk/bps_fbi_sp_ecoli","last_synced_at":"2026-01-30T08:11:37.847Z","repository":{"id":233917390,"uuid":"787839215","full_name":"ssi-dk/bps_fbi_sp_ecoli","owner":"ssi-dk","description":"Ecoli species specific scripts in nbdev2 format.","archived":false,"fork":false,"pushed_at":"2024-07-25T12:24:42.000Z","size":259,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-10T18:44:38.254Z","etag":null,"topics":["bps","ecoli","fbi","nbdev"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/ssi-dk.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":"2024-04-17T09:26:48.000Z","updated_at":"2024-07-25T12:24:46.000Z","dependencies_parsed_at":"2024-07-25T14:09:34.040Z","dependency_job_id":null,"html_url":"https://github.com/ssi-dk/bps_fbi_sp_ecoli","commit_stats":null,"previous_names":["ssi-dk/bps_fbi_sp_ecoli"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ssi-dk%2Fbps_fbi_sp_ecoli","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ssi-dk%2Fbps_fbi_sp_ecoli/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ssi-dk%2Fbps_fbi_sp_ecoli/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ssi-dk%2Fbps_fbi_sp_ecoli/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ssi-dk","download_url":"https://codeload.github.com/ssi-dk/bps_fbi_sp_ecoli/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243974998,"owners_count":20377486,"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":["bps","ecoli","fbi","nbdev"],"created_at":"2024-09-30T16:18:59.512Z","updated_at":"2026-01-30T08:11:32.814Z","avatar_url":"https://github.com/ssi-dk.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# bps_fbi_sp_ecoli\n\n\n\u003c!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! --\u003e\n\n[![PyPI\nversion](https://badge.fury.io/py/bps-fbi-sp-ecoli.svg)](https://badge.fury.io/py/bps-fbi-sp-ecoli)\n[![License:\nMIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![Anaconda-Server\nBadge](https://anaconda.org/kalilamali/bps_fbi_sp_ecoli/badges/version.svg)](https://anaconda.org/kalilamali/bps_fbi_sp_ecoli)\n\n## Quick start\n\n``` bash\n# Type\nfbi_run_ecolityping -h\n# Process\nfbi_run_postecolityping -h\n# Summarize\n! fbi_run_qcecolisummary -h\n```\n\n## Installation\n\n### Pip\n\nNote that this program requires KMA, which is not available on pip. you\nwould need to install it via [conda](https://anaconda.org/bioconda/kma)\nor [github](https://bitbucket.org/genomicepidemiology/kma/src/master/).\n\n``` bash\nconda create /.venv python=3.11\npip install bps_fbi_sp_ecoli\nconda install bioconda::kma\n```\n\n### Conda\n\n``` bash\nconda create /.venv python=3.11\nconda install kalilamali::bps_fbi_sp_ecoli\npip install openpyxl pandas envyaml pandas requests python-dotenv\n```\n\n## Source\n\n``` bash\n# Clone this repo\ngit clone https://github.com/ssi-dk/https://github.com/ssi-dk/bps_fbi_sp_ecoli.git\n# Create an environment with the required tools with conda\nconda create --name ecoli_pipeline kma python=3.11\n# Activate the environment\nconda activate ecoli pipeline\n# Install pip requirements\npip install -r requirements.tx\n```\n\n## How to use\n\nDetermines the serotype and virulence in ecoli through kmer alignment\n\n``` python\n! fbi_run_ecolityping -h\n```\n\n    usage: fbi_run_ecolityping [-h] [--input INPUT] [--sample_sheet SAMPLE_SHEET]\n                               [--output OUTPUT] [--db_path DB_PATH] [--db_update]\n                               [--kma_path KMA_PATH] [--command_file COMMAND_FILE]\n                               [--execute] [--to_stdout] [--overwrite]\n                               [--config_file CONFIG_FILE]\n\n    This program takes as input a folder containing fastq.gz files and a\n    sample_sheet containing SampleID Organism SupplyingLab ecoli1 Ecoli FBI and\n    allows you to run ecolityping.py on all Ecoli samples.\n\n    options:\n      -h, --help                   show this help message and exit\n      --input INPUT                Path to input folder that contains the .fastq.gz\n                                   files\n      --sample_sheet SAMPLE_SHEET  Name of the sample_sheet file\n      --output OUTPUT              Path to the output directory\n      --db_path DB_PATH            Path to db folder that contains the indexed\n                                   database files e.g., file.comp.b, file.fsa,\n                                   file.index.db, file.lenght.b, file.name,\n                                   file.seq.b\n      --db_update                  Option to build/update the database (default:\n                                   False)\n      --kma_path KMA_PATH          Path to kma program\n      --command_file COMMAND_FILE  Path to file to write commands to\n      --execute                    Run commands in command file (default: False)\n      --to_stdout                  If true, will write to stdout instead of file,\n                                   mutually exclusive with output_file (default:\n                                   False)\n      --overwrite                  If true, will overwrite output_file if it exists\n                                   (default: False)\n      --config_file CONFIG_FILE    Config file to overwrite default settings, arg\n                                   parse values will override config file values,\n\n``` python\n! fbi_run_postecolityping -h\n```\n\n    usage: fbi_run_postecolityping [-h] [--input INPUT]\n                                   [--sample_sheet SAMPLE_SHEET] [--output OUTPUT]\n                                   [--command_file COMMAND_FILE] [--execute]\n                                   [--to_stdout] [--overwrite]\n                                   [--config_file CONFIG_FILE]\n\n    This program takes as input a folder containing .tsv files and allows you to run\n    postecolityping.py on all Ecoli samples.\n\n    options:\n      -h, --help                   show this help message and exit\n      --input INPUT                Path to input folder that contains the results of\n                                   kma matching against the ecoligenes db (the\n                                   folder)\n      --sample_sheet SAMPLE_SHEET  Name of the sample_sheet file\n      --output OUTPUT              Path to the output directory\n      --command_file COMMAND_FILE  Path to file to write commands to\n      --execute                    Run commands in command file (default: False)\n      --to_stdout                  If true, will write to stdout instead of file,\n                                   mutually exclusive with output_file (default:\n                                   False)\n      --overwrite                  If true, will overwrite output_file if it exists\n                                   (default: False)\n      --config_file CONFIG_FILE    Config file to overwrite default settings, arg\n                                   parse values will override config file values,\n\n``` python\n! fbi_run_qcecolisummary -h\n```\n\n    usage: fbi_run_qcecolisummary [-h] [--input INPUT] [--output OUTPUT]\n                                  [--command_file COMMAND_FILE] [--execute]\n                                  [--to_stdout] [--overwrite]\n                                  [--config_file CONFIG_FILE]\n\n    This program takes as input a folder containing .tsv files and allows you to run\n    qcecolisummary.py on all Ecoli samples.\n\n    options:\n      -h, --help                   show this help message and exit\n      --input INPUT                Path to input folder that contains the results of\n                                   kma matching against the ecoligenes db (the\n                                   folder)\n      --output OUTPUT              Path to the output directory\n      --command_file COMMAND_FILE  Path to file to write commands to\n      --execute                    Run commands in command file (default: False)\n      --to_stdout                  If true, will write to stdout instead of file,\n                                   mutually exclusive with output_file (default:\n                                   False)\n      --overwrite                  If true, will overwrite output_file if it exists\n                                   (default: False)\n      --config_file CONFIG_FILE    Config file to overwrite default settings, arg\n                                   parse values will override config file values,\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fssi-dk%2Fbps_fbi_sp_ecoli","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fssi-dk%2Fbps_fbi_sp_ecoli","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fssi-dk%2Fbps_fbi_sp_ecoli/lists"}