microbetag.genres
=================

.. py:module:: microbetag.genres






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

.. py:class:: GEMSReconstruction(config)

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


   .. py:method:: rast_annotate_genomes()

      Pool for running rast annotations for a list of bins



   .. py:method:: 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



   .. py:method:: 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..



   .. py:method:: reconstruct_a_model(annotation_faa)

      Build a Genome Scale reconstruction using ModelSEEDpy and the BIN annotations



   .. py:method:: 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!



   .. py:method:: 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.



   .. py:method:: run_carve(faa_files, dna=False)

      Build a GEM using carveme for a list of



   .. py:method:: fgs_annotate_genomes()

      Use FragGeneScan to get .faa files.



.. py:function:: fire_microbetag(yaml_file)