GTDB Taxonomy Data Processing in Python

The provided Python code processes GTDB (Genome Taxonomy Database) taxonomy data. It includes functions for loading taxonomy data, writing blank taxdump files, and manipulating a graph representation of the taxonomy.

The load_gtdb_tax function loads GTDB taxonomy data from an input file into a graph object. It reads each line of the file, parses the taxonomy information, and adds vertices and edges to the graph to represent the taxonomic relationships.

The write_blank_dmp function creates a blank taxdump file, which is a file used in taxonomic classification. It takes an output file name and an optional output directory and writes a blank file with the specified name.

The main function orchestrates the data processing. It creates a graph, loads taxonomy data from input files using load_gtdb_tax, writes output files for the graph (names.dmp and nodes.dmp), generates a standard table of taxIDs, and appends data to the table if specified. Finally, it writes blank delnodes.dmp and merged.dmp files using write_blank_dmp.

The code also includes an if __name__ == '__main__': block to ensure execution only when run directly.

Overall, this code provides a framework for working with GTDB taxonomy data in Python, loading it into a graph representation, generating taxdump files, and creating a standard table of taxIDs.