BCCDC-PHL FluViewer

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fluviewer.fluviewer

This module controls the overall flow of analysis by running each analysis stage.

It runs the following analysis stages:

0. Read Normalization

1. Assemble Contigs

2. BLAST Contigs

3. Scaffolding

4. Read Mapping

5. Variant Calling

6. Consensus Calling

7. Summary Reporting

fluviewer.analysis

This module includes the steps required for each analysis stage.

fluviewer.database

This module includes functions used to check the integrity of the FluViewer database prior to analysis.

fluviewer.parsers

This module includes functions related to parsing output files.

fluviewer.parsers.parse_bbnorm_log(bbnorm_log_path: Path) → dict

Parse the log file generated by BBnorm.

Parameters

bbnorm_log_path (str) – The path to the log file generated by BBnorm.

Returns

A dictionary with the parsed log file.

Return type

dict

fluviewer.parsers.parse_contig_alignment(alignment_path: Path) → list[dict]

Parse the alignment file and return a list of dictionaries representing the alignment of contigs to the scaffold.

Parameters

alignment_path (Path) – The path to the alignment file.

Returns

A list of dictionaries representing the alignment of contigs to the scaffold. Keys are ‘id’, ‘seq’, ‘matches’.

Return type

list[dict]

fluviewer.parsers.parse_scaffolds(scaffolds_path: Path, segment_to_parse: str) → dict

Parse the scaffolds file and return a dictionary of scaffold_id -> scaffold_sequence.

Parameters

• scaffolds_path (Path) – The path to the scaffolds file.

• segment (str) – The segment to parse (e.g. ‘HA’).

Returns

A dictionary with the parsed scaffold sequence. Keys are ‘id’, ‘segment’, ‘seq’ and ‘matches’.

Return type

dict

fluviewer.report

This module includes functions related to building the final summary report.

fluviewer.plots

This module includes functions related to generating plots to visualize FluViewer outputs.

fluviewer.cli_args

This module includes functions related to parsing and validating command-line arguments.

fluviewer.cli_args.parse_args()

Parse command line arguments using argparse.

Returns

Dictionary of arguments and their values.

Return type

dict

fluviewer.cli_args.validate_args(args)

Validate the arguments provided by the user.

Parameters

args (argparse.Namespace) – Dictionary of arguments and their values.

fluviewer.logging_config

This module includes functions related to logging configuration.

fluviewer.logging_config.configure_logging(log_level, log_file)

Configure logging to log to stderr and args.outdir/logs/fluviewer.log. Should configure in such a way that all other modules can call logging.getLogger(__name__) and have the same log settings.