:tocdepth: 3

.. _guppy_mft:

===
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 :doc:`guppy_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.