trace_filter_advanced

Reliability status: development

Advanced script based on trace_filter.

usage: trace_filter_advanced [-h] [-F ROOTFOLDER] [-O OUTPUT] [--input INPUT]
                             [--overlapping_threshold OVERLAPPING_THRESHOLD]
                             [--N_barcodes N_BARCODES] [--pipe]
                             [--output_format {png,svg,pdf}]

Named Arguments

-F, --rootFolder

Folder with images

-O, --output

Tag to add to the output file. Default = filtered

--input

Name of input trace file.

--overlapping_threshold

overlapping threshold. Default = 0.030

--N_barcodes

minimum_number_barcodes. Default = 2

--pipe

inputs Trace file list from stdin (pipe)

Default: False

--output_format

Possible choices: png, svg, pdf

Output image format. Default = png.

Default: 'png'

Output Files

For each trace file analyzed, the script generates:

[output]/[tracefile]_[output].ecsv: Filtered trace table saved in the folder selected with --output (default folder/tag: filtered).
[output]/trace_stat_[tag].[format]: Trace-statistics diagnostic plot written during advanced filtering.
[output]/pairwise_distance_stat.[format]: Pairwise-distance threshold diagnostic plot written when pairwise-distance statistics are saved.
[output]/duplicated_bc_pwd_stat.[format]: Diagnostic plot for duplicated-barcode pairwise-distance statistics.

Examples

trace_filter_advanced --help

Notes

See the command-line reference above for the complete option list.