A toolbox to check whether files follow a predefined schema.
Project description
igs-toolbox
Description
This Python package contains tools to check whether files follow predefined schemas of the IGS project. Currently, only a JSON validator is implemented, but the idea is that it will be extended to more applications related to the IGS project in the future.
Installation
igs-toolbox is installable using pip.
pip install igs-toolbox
Usage
All tools can be used directly through the commandline.
jsonChecker
usage: jsonChecker [-h] -i INPUT
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Filepath to json file.
convertSeqMetadata
The method to convert the metadata table into JSONs for each sample. This inlcudes a validation to check if the IGS metadata scheme is matched.
Usage: convertSeqMetadata [OPTIONS]
Convert table of seq metadata to json files.
Options:
-i, --input FILE Path to input excel or csv/tsv file.
[required]
-o, --output DIRECTORY Path to output folder for json files.
[required]
-l, --log_file FILE Path to log file. [default:
convertSeqMetadata_2023-12-01T09-56-04.log]
--version
--install-completion [bash|zsh|fish|powershell|pwsh]
Install completion for the specified shell.
--show-completion [bash|zsh|fish|powershell|pwsh]
Show completion for the specified shell, to
copy it or customize the installation.
--help Show this message and exit.
Example:
convertSeqMetadata -i IGS_Metadata.xlsx -o out/
readQR
The method readQR reads the Meldungsquittung and extracts the MeldungsID.
Poppler is required to read the pdfs
conda install poppler
or
mamba install poppler
or
apt install poppler-utils
usage: readQR [-h] [--version] [file ...]
positional arguments:
file
options:
-h, --help show this help message and exit
--version show program's version number and exit
Example:
readQR *.pdf
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