filter-features: Filter fragments in tree from table.¶

Docstring:

Usage: qiime fragment-insertion filter-features [OPTIONS]

Filters fragments not inserted into a phylogenetic tree from a feature-
table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
get inserted by SEPP into a reference phylogeny. To be able to use the
feature-table for downstream analyses like computing Faith's PD or
UniFrac, the feature-table must be cleared of fragments that are not part
of the phylogenetic tree, because their path length can otherwise not be
determined. Typically, the number of rejected fragments is low (<= 10),
but it might be worth to inspect the ratio of reads assigned to those
rejected fragments.

Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
A feature-table which needs to filtered down to those
fragments that are contained in the tree, e.g. result
of a Deblur or DADA2 run.                    [required]
--i-tree ARTIFACT    The tree resulting from inserting fragments into a
Phylogeny[Rooted]  reference phylogeny, i.e. the output of function 'sepp'
[required]
Outputs:
--o-filtered-table ARTIFACT FeatureTable[Frequency]
The input table minus those fragments that were not
part of the tree. This feature-table can be used for
downstream analyses like phylogenetic alpha- or beta-
diversity computation.                       [required]
--o-removed-table ARTIFACT FeatureTable[Frequency]
Those fragments that got removed from the input table,
because they were not part of the tree. This table is
mainly used for quality control, e.g. to inspect the
ratio of removed reads per sample from the input table.
You can ignore this table for downstream analyses.
[required]
Miscellaneous:
--output-dir PATH    Output unspecified results to a directory
--verbose / --quiet  Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--examples           Show usage examples and exit.
--citations          Show citations and exit.
--help               Show this message and exit.

Import:

from qiime2.plugins.fragment_insertion.methods import filter_features


Docstring:

Filter fragments in tree from table.

Filters fragments not inserted into a phylogenetic tree from a feature-
table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
get inserted by SEPP into a reference phylogeny. To be able to use the
feature-table for downstream analyses like computing Faith's PD or UniFrac,
the feature-table must be cleared of fragments that are not part of the
phylogenetic tree, because their path length can otherwise not be
determined. Typically, the number of rejected fragments is low (<= 10), but
it might be worth to inspect the ratio of reads assigned to those rejected
fragments.

Parameters
----------
table : FeatureTable[Frequency]
A feature-table which needs to filtered down to those fragments that
are contained in the tree, e.g. result of a Deblur or DADA2 run.
tree : Phylogeny[Rooted]
The tree resulting from inserting fragments into a reference phylogeny,
i.e. the output of function 'sepp'

Returns
-------
filtered_table : FeatureTable[Frequency]
The input table minus those fragments that were not part of the tree.
This feature-table can be used for downstream analyses like
phylogenetic alpha- or beta- diversity computation.
removed_table : FeatureTable[Frequency]
Those fragments that got removed from the input table, because they
were not part of the tree. This table is mainly used for quality
control, e.g. to inspect the ratio of removed reads per sample from the
input table. You can ignore this table for downstream analyses.