bioprov.workflows package¶
Submodules¶
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.
- __init__()¶
- 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.
- Parameters
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.
- Returns
- 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.
- __init__()¶
- parse_options(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.
- bioprov.workflows.workflows.blastn_alignment(**kwargs)¶
- bioprov.workflows.workflows.genome_annotation(**kwargs)¶