README.md

bps_fbi_sp_ecoli

Quick start

# 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 or github.

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

Conda

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

Source

# 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

! 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,

! 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,

! 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,