From b70e8f1b058c0437aa7f7209659c297e03a05791 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Tue, 5 Mar 2024 17:19:08 -0800 Subject: [PATCH 1/2] Add guide on filtering and subsampling Uses a snippet from the Augur docs. --- .gitignore | 1 + src/conf.py | 2 ++ src/fetch-docs.py | 1 + .../bioinformatics/filtering-and-subsampling.rst | 11 +++++++++++ src/guides/bioinformatics/index.rst | 1 + 5 files changed, 16 insertions(+) create mode 100644 src/guides/bioinformatics/filtering-and-subsampling.rst diff --git a/.gitignore b/.gitignore index a86f89b8..155988ba 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,4 @@ src/guides/bioinformatics/translate_ref.md src/guides/bioinformatics/vcf_input.md src/guides/communicate/create-pdf.md src/guides/communicate/narratives-intro.md +src/snippets/filtering-and-subsampling.rst diff --git a/src/conf.py b/src/conf.py index 15b73f5f..25ef461d 100644 --- a/src/conf.py +++ b/src/conf.py @@ -82,6 +82,8 @@ 'augur': ('https://docs.nextstrain.org/projects/augur/page/', None), 'auspice': ('https://docs.nextstrain.org/projects/auspice/page/', None), 'cli': ('https://docs.nextstrain.org/projects/cli/page/', None), + # For externally sourced snippets that reference this docs project + 'docs.nextstrain.org': ('https://docs.nextstrain.org/page/', None), 'nextclade': ('https://docs.nextstrain.org/projects/nextclade/page/', None), 'ncov': ('https://docs.nextstrain.org/projects/ncov/page/', None) } diff --git a/src/fetch-docs.py b/src/fetch-docs.py index 985212b0..f5d78df1 100755 --- a/src/fetch-docs.py +++ b/src/fetch-docs.py @@ -22,6 +22,7 @@ f'{augur_url}faq/fasta_input.md': 'guides/bioinformatics/fasta_input.md', f'{augur_url}faq/seq_traits.md': 'guides/bioinformatics/seq_traits.md', f'{augur_url}examples/examples.rst': 'guides/bioinformatics/examples.rst', + f'{augur_url}usage/cli/snippets/filtering-and-subsampling.rst': 'snippets/filtering-and-subsampling.rst', } if __name__ == '__main__': diff --git a/src/guides/bioinformatics/filtering-and-subsampling.rst b/src/guides/bioinformatics/filtering-and-subsampling.rst new file mode 100644 index 00000000..4522e63a --- /dev/null +++ b/src/guides/bioinformatics/filtering-and-subsampling.rst @@ -0,0 +1,11 @@ +========================= +Filtering and Subsampling +========================= + +Below are some examples of using :doc:`augur filter ` to +sample data. + +.. contents:: Table of Contents + :local: + +.. include:: ../../snippets/filtering-and-subsampling.rst diff --git a/src/guides/bioinformatics/index.rst b/src/guides/bioinformatics/index.rst index 97de1d4d..642e70a2 100644 --- a/src/guides/bioinformatics/index.rst +++ b/src/guides/bioinformatics/index.rst @@ -11,6 +11,7 @@ How-to guides for performing bioinformatic anaylses with Nextstrain. :caption: Table of contents defining-clades + filtering-and-subsampling augur_snakemake missing-sequence-data translate_ref From 1c2f230a6631751d3f9244f709ae250655e2e457 Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Thu, 7 Mar 2024 10:41:27 -0800 Subject: [PATCH 2/2] Move defining-clades guide lower in sidebar Put it below guides related to augur filter/align, and closer to other guides relating to augur export. --- src/guides/bioinformatics/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/guides/bioinformatics/index.rst b/src/guides/bioinformatics/index.rst index 642e70a2..b5d4b751 100644 --- a/src/guides/bioinformatics/index.rst +++ b/src/guides/bioinformatics/index.rst @@ -10,12 +10,12 @@ How-to guides for performing bioinformatic anaylses with Nextstrain. :titlesonly: :caption: Table of contents - defining-clades filtering-and-subsampling augur_snakemake missing-sequence-data translate_ref import-beast + defining-clades colors lat_longs vcf_input