samsifter.stats package

Stand-alone scripts used in post-processing of workflow statistics.

The scripts in this package are optionally executed after a SamSifter workflow to compile temporary statistics files.

compile_stats module

Compilation of statistics for a SAM file.

Usually executed after processing a SAM file with a workflow containing steps that produce temporary statistics files, eg. the samsifter.tools.count_taxon_reads module. The script takes all temporary files in the working directory, sorts them by their filenames and appends their values as new columns to statistics spreadsheet named after the original input file.

Both the SamSifter GUI as well as the Bash scripts exported from it will execute this script by default and remove all temporary statistics files when done.

Note

See the script enrich_summary for details on how to enrich the resulting file with data from external databases like IMG/M.

See the script summarize_stats for details on how to summarize multiple statistics files to quickly inspect the results of a batch run.

main()

Executes the compilation of temporary statistics files.

See --help for details on expected arguments.

summarize_stats module

Compilation of statistics for multiple files into a summary spreadsheet.

Usually executed after batch processing of multiple SAM files with the same workflow. The script takes the final read count of each statistics file and adds it to a new spreadsheet using the input filename as header.

All Bash scripts exported from the SamSifter GUI that are processing multiple files (sequential or parallel processing mode) will execute this script by default and remove all temporary statistics files when done.

Note

See the script enrich_summary.py for details on how to enrich this summary with data from external databases like IMG/M.

main()

Executes the summarization of multiple statistics files.

See --help for details on expected arguments.