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).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--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.
