…dmp and merged.dmp are out of sync with nr.gz

merge nodes when databases out of sync.

…2020.

…g. Renamed 'projects' to 'workspace' to avoid confusion with 'project'. test metagenome.config file has been updated with respective files & parameters. Reconfigured logger to stream info and write debug level to timestamped log file. Added exceptions. to be used across autometa pipeline.

…etrieves versions from each executable dependency in environ.py. This is used in prodigal to parse corresponding to the prodigal version. I.e. 2.5 differs from version >=2.6. Prodigal now will parse ORF headers and convert contigs to ORF headers according to version available. Default config now has versions section and generated config files now contain versions section related to executable dependencies. Renamed 'new_workspace' in user.py to 'new_project' as this is more appropriate.

…es.py for handling databases config. Default behavior is to download and format required databases. Changed flag to flag to be more clear. autometa will print an issue request to the user upon any exceptions being encountered (NOT KeyboardInterrupt.. Although this will also be logged). Logging behavior changed slightly, where user can specify level (default is INFO) and path to log file. binning call has been moved to user.py. autometa.config imports in user.py have been removed and general autometa.config module is imported via to perform respective func call.

…en checking dependencies. Executable versions are now logged in debug info. log is now only written when flag is supplied. Timestamped log has been commented out. In the future, this could be a flag to log each run via a timestamped log. in databases now only returns the config and the method of databases is used when checking dependencies.

…gram is provided as input. Updated respective files using this function. This should be clearer than returning a dict of the program passed in as key and removes redundant calls to pass in the program as input and then again as a key to retrieve the version value.

…ip performing check to place appropriate metagenome number and just return 1.

… a bug fix related to exception hierarchy. changed timeit logging message format. Respective exception handling updatedin metagenome.py

…Note: entire pipeline currently assumes orf calling was performed using prodigal. Update to template.py where ArgumentParser now has default description, where previously this was by default usage. (Which the usage by default should be the name of the script). Updates to respective files where ORF to contig translations are necessary.

… 1.0. in kmers and recursive_dbscan. Updated main function for recursive dbscan with required coverage table input and subsetting taxonomy by the provided domain. Datatype conversion in pandas dataframes are now performed to optimize space in mag.py and recursive_dbscan.py. Added script description to coverage.py and removed unused exception handling in docstring. Renamed bedtools column 'breadth' to 'depth_fraction' and 'total_breadth' to 'depth_product'. Added KmerFormatError in docstring in kmers.load() func. Updated docstring in autometa.config.environ.find_executables()

… list handling for multiple reads files in input. Added fasta format check and simple fasta parser from Biopython for performance and Exception handling. Docstrings noting where discussions should be placed on readthedocs relating to specific autometa functionality.