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Export a preset file given the preset name or source file and a set of mix-ins

This command can help to understand structure of preset or compare presets.

Exported file may be a starting point for writing custom preset.

Command line options

mixcr exportPreset
    (--preset-name <preset> | --mixcr-file <input.(vdjca|clns|clna)>) 


    # mix-ins
    [--add-step <step>] 
    [--remove-step <step>] 
    [-s <species>] 
    [-b <library>] 
    [--sample-table sample_table.tsv] 
    [--floating-left-alignment-boundary [<anchor_point>]] 
    [--rigid-left-alignment-boundary [<anchor_point>]] 
    [--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
    [--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)]] 
    [--tag-pattern <pattern>] 
    [--limit-input <n>] 
    [--assemble-clonotypes-by <gene_features>] 
    [--split-clones-by <gene_type>]... 
    [--dont-split-clones-by <gene_type>]... 
    [--assemble-contigs-by <gene_features>] 
    [--prepend-export-clones-field <field> [<param>...]]... 
    [--append-export-clones-field <field> [<param>...]]... 
    [--prepend-export-alignments-field <field> [<param>...]]... 
    [--append-export-alignments-field <field> [<param>...]]... 
    [--add-export-clone-table-splitting <(geneLabel|tag):key>]
    [--add-export-clone-grouping <(geneLabel|tag):key>] 
    [-M <key=value>]... 

    # output
Path where to write preset yaml file. Will write to output if omitted.
--preset-name <preset>
Preset name to export (see complete list of available presets).
--mixcr-file <input.(vdjca|clns|clna)>
File that was processed by MiXCR.
Don't validate preset before export.
-f, --force-overwrite
Force overwrite of output file(s).
-nw, --no-warnings
Suppress all warning messages.
Verbose messages.
-h, --help
Show this help message and exit.

In addition to these parameters, any of the available mix-in options may be additionally specify at exportPreset.


> mixcr exportPreset --mixcr-file result.vdjca preset.yaml

Result is preset file used to process result.vdjca. The same may be applied to *.clns or *.clna files.

> mixcr exportPreset --preset-name 10x-vdj-bcr preset.yaml

Result is preset file of 10x-vdj-bcr preset.

> mixcr exportPreset --preset-name generic-tcr-amplicon \ 
    --species hs \
    --dna \
    --floating-left-alignment-boundary \
    --floating-right-alignment-boundary J \

Result is generic-tcr-amplicon preset with all required mixins set.

> mixcr exportPreset --preset-name generic-tcr-amplicon \
    --no-validation \

Result is generic-tcr-amplicon preset without some required mixins. Useful for comparing presets or writing custom preset.

> diff \
    <(mixcr exportPreset --preset-name 10x-vdj-bcr) \
    <(mixcr exportPreset --preset-name 10x-vdj-tcr)

Comparing two presets between each other. Alternatively, one can export them in separate files and use some other tool for comparison.