bps-fbi-sp-ecoli 0.0.7
Species specific scripts for ecoli
License: MIT License
Requires Python: >=3.7
Keywords: nbdev jupyter notebook python

# bps_fbi_sp_ecoli


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## Quick start

``` bash
# Type
fbi_run_ecolityping -h
# Process
fbi_run_postecolityping -h
# Summarize
! fbi_run_qcecolisummary -h
```

## Installation

### Pip

Note that this program requires KMA, which is not available on pip. you
would need to install it via [conda](https://anaconda.org/bioconda/kma)
or [github](https://bitbucket.org/genomicepidemiology/kma/src/master/).

``` bash
conda create /.venv python=3.11
pip install bps_fbi_sp_ecoli
conda install bioconda::kma
```

### Conda

``` bash
conda create /.venv python=3.11
conda install kalilamali::bps_fbi_sp_ecoli
pip install openpyxl pandas envyaml pandas requests python-dotenv
```

## Source

``` bash
# Clone this repo
git clone https://github.com/ssi-dk/https://github.com/ssi-dk/bps_fbi_sp_ecoli.git
# Create an environment with the required tools with conda
conda create --name ecoli_pipeline kma python=3.11
# Activate the environment
conda activate ecoli pipeline
# Install pip requirements
pip install -r requirements.tx
```

## How to use

Determines the serotype and virulence in ecoli through kmer alignment

``` python
! fbi_run_ecolityping -h
```

    usage: fbi_run_ecolityping [-h] [--input INPUT] [--sample_sheet SAMPLE_SHEET]
                               [--output OUTPUT] [--db_path DB_PATH] [--db_update]
                               [--kma_path KMA_PATH] [--command_file COMMAND_FILE]
                               [--execute] [--to_stdout] [--overwrite]
                               [--config_file CONFIG_FILE]

    This program takes as input a folder containing fastq.gz files and a
    sample_sheet containing SampleID Organism SupplyingLab ecoli1 Ecoli FBI and
    allows you to run ecolityping.py on all Ecoli samples.

    options:
      -h, --help                   show this help message and exit
      --input INPUT                Path to input folder that contains the .fastq.gz
                                   files
      --sample_sheet SAMPLE_SHEET  Name of the sample_sheet file
      --output OUTPUT              Path to the output directory
      --db_path DB_PATH            Path to db folder that contains the indexed
                                   database files e.g., file.comp.b, file.fsa,
                                   file.index.db, file.lenght.b, file.name,
                                   file.seq.b
      --db_update                  Option to build/update the database (default:
                                   False)
      --kma_path KMA_PATH          Path to kma program
      --command_file COMMAND_FILE  Path to file to write commands to
      --execute                    Run commands in command file (default: False)
      --to_stdout                  If true, will write to stdout instead of file,
                                   mutually exclusive with output_file (default:
                                   False)
      --overwrite                  If true, will overwrite output_file if it exists
                                   (default: False)
      --config_file CONFIG_FILE    Config file to overwrite default settings, arg
                                   parse values will override config file values,

``` python
! fbi_run_postecolityping -h
```

    usage: fbi_run_postecolityping [-h] [--input INPUT]
                                   [--sample_sheet SAMPLE_SHEET] [--output OUTPUT]
                                   [--command_file COMMAND_FILE] [--execute]
                                   [--to_stdout] [--overwrite]
                                   [--config_file CONFIG_FILE]

    This program takes as input a folder containing .tsv files and allows you to run
    postecolityping.py on all Ecoli samples.

    options:
      -h, --help                   show this help message and exit
      --input INPUT                Path to input folder that contains the results of
                                   kma matching against the ecoligenes db (the
                                   folder)
      --sample_sheet SAMPLE_SHEET  Name of the sample_sheet file
      --output OUTPUT              Path to the output directory
      --command_file COMMAND_FILE  Path to file to write commands to
      --execute                    Run commands in command file (default: False)
      --to_stdout                  If true, will write to stdout instead of file,
                                   mutually exclusive with output_file (default:
                                   False)
      --overwrite                  If true, will overwrite output_file if it exists
                                   (default: False)
      --config_file CONFIG_FILE    Config file to overwrite default settings, arg
                                   parse values will override config file values,

``` python
! fbi_run_qcecolisummary -h
```

    usage: fbi_run_qcecolisummary [-h] [--input INPUT] [--output OUTPUT]
                                  [--command_file COMMAND_FILE] [--execute]
                                  [--to_stdout] [--overwrite]
                                  [--config_file CONFIG_FILE]

    This program takes as input a folder containing .tsv files and allows you to run
    qcecolisummary.py on all Ecoli samples.

    options:
      -h, --help                   show this help message and exit
      --input INPUT                Path to input folder that contains the results of
                                   kma matching against the ecoligenes db (the
                                   folder)
      --output OUTPUT              Path to the output directory
      --command_file COMMAND_FILE  Path to file to write commands to
      --execute                    Run commands in command file (default: False)
      --to_stdout                  If true, will write to stdout instead of file,
                                   mutually exclusive with output_file (default:
                                   False)
      --overwrite                  If true, will overwrite output_file if it exists
                                   (default: False)
      --config_file CONFIG_FILE    Config file to overwrite default settings, arg
                                   parse values will override config file values,