Metadata-Version: 2.1
Name: bps_fbi_sp_ecoli
Version: 0.0.3
Summary: Species specific scripts for ecoli
Home-page: https://github.com/ssi-dk/bps_fbi_sp_ecoli
Author: kalilamali
Author-email: kloc@ssi.dk
License: MIT License
Keywords: nbdev jupyter notebook python
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: fastcore
Requires-Dist: python-dotenv
Requires-Dist: envyaml
Requires-Dist: pandas
Requires-Dist: requests
Requires-Dist: openpyxl
Provides-Extra: dev

# bps_fbi_sp_ecoli


<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

## Install

``` sh
pip install bps_fbi_sp_ecoli
```

## How to use

Determines the serotype and virulence in ecoli through kmer alignment

``` python
! FBI_run_bifrostecolipostkma -h
```

``` python
#! FBI_run_bifrostecolipostkma --input input/231116_CUSTOM_SSIFBI_ECOLI --sample_sheet sample_sheet.xlsx --output output/231116_CUSTOM_SSIFBI_ECOLI --command_file output/231116_CUSTOM_SSIFBI_ECOLI/run_bifrostecolipostkma.tsv --execute
```

``` python
! FBI_run_qcecolisummary -h
```

``` python
#! FBI_run_bifrostecolipostkma --input input/231116_CUSTOM_SSIFBI_ECOLI --sample_sheet sample_sheet.xlsx --output output/231116_CUSTOM_SSIFBI_ECOLI --command_file output/231116_CUSTOM_SSIFBI_ECOLI/run_bifrostecolipostkma.tsv --execute
```
