Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/ssi-dk/bps_fbi_sp_ecoli
Ecoli species specific scripts in nbdev2 format.
https://github.com/ssi-dk/bps_fbi_sp_ecoli
bps ecoli fbi nbdev
Last synced: 2 months ago
JSON representation
Ecoli species specific scripts in nbdev2 format.
- Host: GitHub
- URL: https://github.com/ssi-dk/bps_fbi_sp_ecoli
- Owner: ssi-dk
- License: mit
- Created: 2024-04-17T09:26:48.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2024-07-25T12:24:42.000Z (5 months ago)
- Last Synced: 2024-10-22T05:37:22.574Z (2 months ago)
- Topics: bps, ecoli, fbi, nbdev
- Language: Jupyter Notebook
- Homepage:
- Size: 253 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# bps_fbi_sp_ecoli
[](https://badge.fury.io/py/bps-fbi-sp-ecoli)
[](https://opensource.org/licenses/MIT)
[](https://anaconda.org/kalilamali/bps_fbi_sp_ecoli)
## 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,