Fork me on GitHub

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

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.

Options:
  --i-table ARTIFACT PATH 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 PATH Phylogeny[Rooted]
                                  The tree resulting from inserting fragments
                                  into a reference phylogeny, i.e. the output
                                  of function 'sepp'  [required]
  --o-filtered-table ARTIFACT PATH 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 if not passing
                                  --output-dir]
  --o-removed-table ARTIFACT PATH 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 if not
                                  passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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.