microbetag.tools

Module Contents

microbetag.tools.run_phylomint(config)

Invoke PhyloMInt as edited from microbetag team to support parallel calculation of the seed and non seed sets and save corresponding sets to json files.

microbetag.tools.hmmsearch(params: List)

Function to invoke hmmsearch software.

params: list of parameters to be passed to the hmmsearch function.

microbetag.tools.run_prodigal(fasta, basename, outdir)

Function to predict ORFs using Prodigal. By default outdir is the ORFs folder fna FASTA nucleic acid Used generically to specify nucleic acids ffn FASTA nucleotide of gene regions Contains coding regions for a genome

microbetag.tools.kegg_annotation(faa, basename, out_dir, db_dir, ko_dic, threads)

Function to perform KEGG annotation. The function invokes hmmsearch.

Inputs:

faa (str): Path to the .faa file of the bin in process basename (str): Bin id out_dir (str): Path to output directory where .hmmout files will be stored db_dir (str): Path to KEGG database directory ko_dic (Dict): threads (int): Number of threads to be used

microbetag.tools.phenotrex_genotype(config)

Get COGs present in your genomes

microbetag.tools.phenotrex_predict(config)

microbetag.tools.run_manta(config)

microbetag.tools.run_flashweave(config)

microbetag.tools.run_faprotax(config)

Run FAPROTAX collapse_table.py script