silvtal / get_core_reactions

Given a folder with eggnog annotation files (multiple genomes), create a consensus annotations file and save a series of core reactions in different formats

core_functions_full.py

Create file with X% consensus annotations ("PCG pangenome"). Save to files parsed list in BiGG/KEGG/EC reaction format.

This script generates a list of core functions for a given phylogenetic core group (PCG). This list is considered that PCG's pangenome, defined as annotations present in at least 90% of available genomes for each PCG. The input for this tool is a path containing .tsv annotation files generated with eggNOG-mapper, for which a consensus annotation file will be generated. The core reactions can be retrieved in KEGG, EC and in BiGG format. A file containing descriptions corresponding to EC and KEGG entries is also generated.

More reactions can be added manually using tools like MetaNetX or by creating custom ko/EC files

Creates consensus annotations from a folder with single genome annotations

Print_unique_functions.ipynb

For each PCG, print all pangenome reactions exclusive to itself.

This script reads the files (either BiGG or KEGG) from the first step and goes through each PCG, comparing its reactions with the reactions of other groups, and keeping track of the unique reactions for each group in a dictionary.

Print_all_descriptions.ipynb

Print all pangenome reactions for each PCG, exclusive or not, alongside a description.

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Example_Goldford

This folder contains the specific version of script #1 used at "Leveraging phylogenetic signal to unravel microbial community function and assembly rules" by Talavera-Marcos, Parras-Moltó and Aguirre de Cárcer