microbetag.tools
================

.. py:module:: microbetag.tools




Module Contents
---------------

.. py:function:: 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.


.. py:function:: hmmsearch(params: List)

   Function to invoke hmmsearch software.

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


.. py:function:: 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


.. py:function:: 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


.. py:function:: phenotrex_genotype(config)

   Get COGs present in your genomes


.. py:function:: phenotrex_predict(config)

   


.. py:function:: run_manta(config)

.. py:function:: run_flashweave(config)

.. py:function:: run_faprotax(config)

   Run FAPROTAX collapse_table.py script