From 717bec1746cb7aaa2591c6d197c80a8ac0137ff4 Mon Sep 17 00:00:00 2001 From: Daniela Perry Date: Tue, 14 Jun 2022 16:00:25 -0700 Subject: [PATCH 1/2] update readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ccce7d5..730c6b3 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/avai ``` qiime katharoseq read_count_threshold \ - --i-table a_genus_level_table.qza \ + --i-table example.qza \ # a_genus_level_table --p-threshold 80 \ --p-control classic \ --p-positive-control-value name_of_controls_in_metadata \ @@ -32,4 +32,4 @@ qiime katharoseq read_count_threshold \ --m-cell-count-column-file your_metadata.tsv \ --m-cell-count-column-column cell_count_variable_in_metadata \ --o-visualization result.qzv -``` +``` \ No newline at end of file From af9ce7ca230764c3200de449db3866cd1199bb29 Mon Sep 17 00:00:00 2001 From: Daniela Perry Date: Tue, 14 Jun 2022 16:23:27 -0700 Subject: [PATCH 2/2] Update readme and setup --- README.md | 23 ++++++++++++++++++----- setup.py | 1 + 2 files changed, 19 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 730c6b3..56d9c49 100644 --- a/README.md +++ b/README.md @@ -14,13 +14,26 @@ pip install -e . ## Use +Computation assumes that the user has classified their 16S features against SILVA, and that the `FeatureTable[Frequency]` has been collapsed to the genus level. Please see the [`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy +classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level. If you need more information on how to process your data, please refer to one of the relevant tutorials that can be found [here](https://docs.qiime2.org/2022.2/tutorials/). + + +## Obtaining a read count threshold + Computation of a minimum read count threshold can be performed with the -`read_count_threshold` plugin action. Computation assumes that the user has -classified their 16S features against SILVA, and that the -`FeatureTable[Frequency]` has been collapsed to the genus level. Please see the -[`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy -classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level. +`read_count_threshold` plugin action. Test data can be found under the `testdata` folder. +``` +qiime katharoseq read_count_threshold \ + --i-table example/example_table_genus.qza \ # a genus level table + --p-threshold 80 \ + --p-control classic \ + --p-positive-control-value katharoseq_control \ # name of controls in metadata + --m-positive-control-column-file example/simple_katharoseq_metadata.tsv \ # your metadata + --m-positive-control-column-column control_or_sample \ # sample type variable in metadata + --m-cell-count-column-file example/simple_katharoseq_metadata.tsv \ + --m-cell-count-column-column max_cell_count \ # cell count variable in metadata + --o-visualization result.qzv ``` qiime katharoseq read_count_threshold \ --i-table example.qza \ # a_genus_level_table diff --git a/setup.py b/setup.py index 8968ecc..c60fec7 100644 --- a/setup.py +++ b/setup.py @@ -26,6 +26,7 @@ }, package_data={ "q2_katharoseq": ['citations.bib'], + "example": ['*'] }, zip_safe=False, install_requires=['scipy',