Comments (6)
Hi @wasade, the tutorial (qiime2/docs#39) is slated for the February release cycle. Thanks!
from q2-feature-table.
So https://docs.qiime2.org/2.0.6/tutorials/table-filtering/ shouldn't be live?
from q2-feature-table.
For a little more context, the URL listed in the help text below is invalid
$ qiime feature-table filter-features --help
Usage: qiime feature-table filter-features [OPTIONS]
Filter features from table based on frequency and/or metadata. Any samples
with a frequency of zero after feature filtering will also be removed. If
no value(s) are provided for max_frequency and/or max_samples, they will
default to infinity (i.e., no maximum frequency and/or sample filter will
be applied).
The where parameter takes a SQLite WHERE clause. See the table filtering
tutorial for additional detail:
https://docs.qiime2.org/2.0.6/tutorials/table-filtering.html
Options:
--i-table PATH Artifact: FeatureTable[Frequency]
[required]
--m-feature-metadata-file PATH Metadata mapping file [optional]
--p-max-frequency INTEGER [optional]
--p-max-samples INTEGER [optional]
--p-min-frequency INTEGER [default: 0]
--p-min-samples INTEGER [default: 0]
--p-where TEXT [optional]
--o-filtered-table PATH Artifact: FeatureTable[Frequency] [required
if not passing --output-dir]
--output-dir DIRECTORY Output unspecified results to a directory
--cmd-config PATH Use config file for command options
--verbose Display verbose output to stdout and/or
stderr during execution of this action.
[default: False]
--help Show this message and exit.
from q2-feature-table.
Right, the tutorial is up there now (https://docs.qiime2.org/2.0.6/tutorials/table-filtering/), but the URL listed in the help text has an extra .html
at the end. I was confused about what you were asking about initially. The fix will be to just drop the suffix in the help text URL. Also, I think this happened because the URL was specified before we actually had a tutorial in place, so this was a bit of a placeholder. Thanks!
from q2-feature-table.
Also, I totally spaced that we decided to update the 2.0.6
docs to include this tutorial. This makes sense though, because the functionality is present in the 2.0.6
release.
from q2-feature-table.
from q2-feature-table.
Related Issues (20)
- Upgrade Summarize Plots to Vega 5
- generalize filter-seqs to operate on aligned sequences (in addition to unaligned sequences)
- IMP: `merge` should accept other feature table types HOT 2
- Add download csv links to Feature Detail and Interactive Sample Detail tabs HOT 1
- Allow table grouping across multiple semantic table types
- qiime feature-table rarefy --p-with-replacement: sum(pvals[:-1]) > 1.0 HOT 7
- in versions 2020.11 and later sample frequency tables have a random ",0" as first row
- Update 'master' branch name to 'main' HOT 2
- Empty cells in numeric metadata column causing error with viewing feature-table.qzv
- Update table heading in `feature-table summarize` result HOT 1
- `transpose` should support `FeatureTable[RelativeFrequency]` HOT 1
- add split-feature-table action
- add optional inputs to `tabulate-seqs` HOT 4
- add new outputs to `summarize`
- minor numeric formatting changes in `summarize` and `summarize-plus`
- IMP: helper method in `filter_seqs` should have an underscore prefix
- BUG: improve error message formatting in `feature-table tabulate-seqs`
- rename `subsample` action to `subsample-ids`
- sample ids not displayed in summarized feature table HOT 3
- BIOM import failed, TypeError: No format: BIOMV210Format HOT 3
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