This tool is used for generation and execution of SPARQL queries for usage in bioinformatics. Currently only UniProt endpoint is supported.
Install dependencies
pip -r requirements.txt
and clone the repository.
Usage: data_collector.py [OPTIONS] CONFIG_PATH
Generate query based on config saved in config_path
Options:
-q, --print-query Toggle to show generated query
--out-path PATH Path where to save result of the query, must have either
csv or xlsx extension
--help Show this message and exit.
Config file is in JSON format with two fields, dataSelector for column selection and dataFilter for filtering.
dataSelector contains columns list which lists selected columns. Currently available values are Protein, ProteinId, Name, Sequence, Reaction.
dataFilter describes how will the data be filtered. The pfams list contains PFAMs that will be included (has to have at least one of them), similarly with supfams. reviewed sets whether to select reviews or unreviewed records. And taxa list contains UniProt IDs of taxas and only proteins that belong to an organism that belongs into at least on of the listed taxa. All fields are optional.
See sample_config.json for example.