mft

mft Multi-Filter and Transform placefiles.

usage: mft [options] placefile[s]

Options

-o	Specify the filename to write to.
--out-dir	Specify the directory to write files to.
--prefix	Specify a string to be prepended to filenames.
--unitize	Make total unit mass per placerun by multiplying with a scalar.
--transform	A transform to apply to the read multiplicities before calculating. Options are ‘log’, ‘unit’, ‘asinh’, and ‘no_trans’. Default is no transform.
--leaf-values	Name of CSV file giving values for the leaves of the tree to use in independent contrasts.

Details

This is the power tool for splitting apart place files and applying mass transforms.

If either the --transform or --unitize flags are specified, then the resulting placefiles will have mass instead of a name list. Otherwise, the output placefiles will have either mass or a name list depending on what the input placefiles had.

To do nothing but transform the input placefiles to placefiles with mass instead of a name list, specify --transform no_trans.

One can use the --leaf-values flag to correct for copy number. This flag runs the internals of indep_c and then divides the masses of the placements by the inferred value, which can be copy number if you supply --leaf-values with a CSV file of copy numbers for reference sequences.