GENESPACE-Companion-Script

This contains a python script developed as a companion to the GENESPACE pan-genome tool to obtain statistics from the output of GENESPACE.

GENESPACE GitHub

GENESPACE Manuscript

Input file

The input file is a TSV file, unique from the standard results/[reference_genome]_pangenome.txt.gz file. This file was generated based on the information provided in Section 9.4 in the official GENESPACE Vignette.

The following code can be run after following GENESPACE's documentation and obtaining the pangenome data.table object.

fwrite(pg, file = 'pangenome.tsv', quote = FALSE, sep = '\t')

Current output statistics

• Total number of single-species orthogroups (one species, at least one gene).
• Total number of singletons (one species, only one gene).
• Number of singletons for each individual gene set.
• Total number of complete orthogroups (each gene set has at least one gene present in the orthogroup).
• Total number of single-copy orthogroups (each gene set has exactly one gene present in the orthogroup).