microbetag.genres

Module Contents

class microbetag.genres.GEMSReconstruction(config)

Class to first RAST annotate and the build Genome Scale Metabolic Reconstructions using modelseedpy

rast_annotate_genomes()

Pool for running rast annotations for a list of bins

rast_annotate_a_genome(bin_filename)

RAST annotate a user’s bin based on: https://www.bv-brc.org/docs/cli_tutorial/rasttk_getting_started.html#the-concept-of-the-genome-typed-object

modelseed_reconstructions()

Pool for running GENREs reconstruction using the final .faa files from the rast_annotate_genomes() function [NOTE] Not to be used for now as the RAST server seems not that stable to have several queries..

reconstruct_a_model(annotation_faa)

Build a Genome Scale reconstruction using ModelSEEDpy and the BIN annotations

recursive_build(model_id, annotation_faa_path, counter=0)

RAST server usually has issues that lead to fail attempts. This recursive function allows the build_metabolic_model() to be performed until the server responses.

[NOTE] We have observed that when MSGenome is initiated in the same function with the MSBuilder, they behave much better!

carve_reconstructions()

Reconstruct a GENRE using CarveMe and a .faa as input. You can get such a file after running RAST annotation or after any gene prediction tool such as Prodigal, FragenScan etc.

run_carve(faa_files, dna=False)

Build a GEM using carveme for a list of

fgs_annotate_genomes()

Use FragGeneScan to get .faa files.

microbetag.genres.fire_microbetag(yaml_file)