diff --git a/docs/astro.config.mjs b/docs/astro.config.mjs index 023d8b660..2cc746842 100644 --- a/docs/astro.config.mjs +++ b/docs/astro.config.mjs @@ -37,6 +37,7 @@ export default defineConfig({ label: 'For users', items: [ { label: 'Introduction', link: '/for-users/introduction/' }, + { label: 'Search sequences', link: '/for-users/search-sequences/' }, { label: 'Edit account', link: '/for-users/edit-account/' }, { label: 'Create and manage groups', link: '/for-users/create-manage-groups/' }, { label: 'Submit sequences', link: '/for-users/submit-sequences/' }, diff --git a/docs/src/content/docs/for-users/search-sequences.md b/docs/src/content/docs/for-users/search-sequences.md new file mode 100644 index 000000000..49f2696fa --- /dev/null +++ b/docs/src/content/docs/for-users/search-sequences.md @@ -0,0 +1,33 @@ +--- +title: Search sequences +--- + +## Mutations + +### Nucleotide mutations and insertions + +A nucleotide mutation has the format `` or ``. A `` can be one of the four nucleotides `A`, `T`, `C`, and `G`. It can also be `-` for deletion and `N` for unknown. For example if the reference sequence is `A` at position 23 both: `23T` and `A23T` will yield the same results. + +If your organism is multi-segmented you must append the name of the segment to the start of the mutation, e.g. `S:23T` and `S:A23T` for a mutation in segment `S`. + +Insertions can be searched for in the same manner, they just need to have `ins_` appended to the start of the mutation. Example `ins_10462:A` or if the organism is multi-segmented `ins_S:10462:A`. + +### Amino acid mutations and insertions + +An amino acid mutation has the format `:` of `:`. A `` can be one of the 20 amino acid codes. It can also be `-` for deletion and `X` for unknown. Example: `E:57Q`. + +Insertions can be searched for in the same manner, they just need to have `ins_` appended to the start of the mutation. Example `ins_NS4B:31:N`. + +### Insertion wildcards + +Loculus supports insertion queries that contain wildcards `?`. For example `ins_S:214:?EP?` will match all cases where segment `S` has an insertion of `EP` between the positions 214 and 215 but also an insertion of other AAs which include the `EP`, e.g. the insertion `EPE` will be matched. + +You can also use wildcards to match any insertion at a given position. For example `ins_S:214:?:` will match any (but at least one) insertion between the positions 214 and 215. + +### Multiple mutations + +Multiple mutation filters can be provided by adding one mutation after the other. + +### Any mutation + +To filter for any mutation at a given position you can omit the ``. diff --git a/website/src/pages/docs/how-to/authentication-api.astro b/website/src/pages/docs/how-to/authentication-api.astro new file mode 100644 index 000000000..d7a795de7 --- /dev/null +++ b/website/src/pages/docs/how-to/authentication-api.astro @@ -0,0 +1,3 @@ +--- +return Astro.redirect('https://loculus.org/for-users/authenticate-via-api/'); +--- diff --git a/website/src/pages/docs/how-to/search-sequences-website.astro b/website/src/pages/docs/how-to/search-sequences-website.astro new file mode 100644 index 000000000..5b2f3be6c --- /dev/null +++ b/website/src/pages/docs/how-to/search-sequences-website.astro @@ -0,0 +1,3 @@ +--- +return Astro.redirect('https://loculus.org/for-users/search-sequences/'); +--- diff --git a/website/src/pages/docs/how-to/search-sequences-website.mdx b/website/src/pages/docs/how-to/search-sequences-website.mdx deleted file mode 100644 index ffa32c6e5..000000000 --- a/website/src/pages/docs/how-to/search-sequences-website.mdx +++ /dev/null @@ -1,3 +0,0 @@ -# How to Search - -Fill this in with tips for your loculus instance.