mft Multi-Filter and Transform placefiles.
usage: mft [options] placefile[s]
| -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. |
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.