bioprov.workflows package


bioprov.workflows.blastn_alignment module

bioprov.workflows.genome_annotation module

bioprov.workflows.KaijuWorkflow module

Class holding the KaijuWorkflow main function and parser.

bioprov.workflows.WorkflowOptionsParser module

Class for parsing command-line options.

Module contents

Module containing preset workflows created with the Workflow class.

class bioprov.workflows.workflows.KaijuWorkflow

Bases: object

Class holding the KaijuWorkflow main function and parser.

description = 'Run Kaiju on metagenomic data and create reports for taxonomic ranks.'
static main(input_file, output_path=None, kaijudb=None, nodes=None, names=None, threads=1, _tag=None, verbose=False, resume=True, kaiju_params='', kaiju2table_params='')

Main function to run the Kaiju workflow.

  • input_file – Input tab delimited file with the columns: ‘sample-id’, ‘R1’, ‘R2’

  • output_path – Directory to create Kaiju output files.

  • kaijudb – Kaiju database file.

  • nodes – Kaiju nodes file.

  • names – Kaiju names file.

  • threads – Number of threads to use with Kaiju.

  • _tag – Tag for Project.

  • verbose – Verbose output.

  • resume – Check for existing files and skip running Kaiju for them.

  • kaiju_params – Parameter string to add to Kaiju command.

  • kaiju2table_params – Parameter string to add to kaiju2table command.


classmethod parser()

Parser for the Kaiju workflow. :return: instance of argparse.ArgumentParser.

class bioprov.workflows.workflows.WorkflowOptionsParser

Bases: object

Class for parsing command-line options.


Parses options and returns correct workflow. :type options: argparse.Namespace :param options: arguments passed by the parser. :return: Runs the specified subparser in options.subparser_name.