# 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
```
usage: FBI_run_bifrostecolipostkma [-h] [--input INPUT]
[--sample_sheet SAMPLE_SHEET]
[--output OUTPUT] [--db_path DB_PATH]
[--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 bifrostecolipostkma.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
--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_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
```
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,
``` 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
```
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