From 2f014238b3ec504323013b10ba10b6094dd43031 Mon Sep 17 00:00:00 2001 From: the-mayer <32186106+the-mayer@users.noreply.github.com> Date: Mon, 7 Oct 2024 20:13:19 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20JRaviLab?= =?UTF-8?q?/MolEvolvR@42c35ff653147ff89c2af00dc2cfce102fdcaeef=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/acc2fa.html | 22 ++--- reference/addLeaves2Alignment.html | 114 ++++++++++++++++++++++ reference/addName.html | 111 ++++++++++++++++++++++ reference/add_leaves.html | 22 +---- reference/add_name.html | 22 +---- reference/convert2TitleCase.html | 84 ++++++++++++++++ reference/convertAlignment2FA.html | 121 ++++++++++++++++++++++++ reference/convert_aln2fa.html | 25 +---- reference/count_to_sunburst.html | 8 +- reference/generateAllAlignments2FA.html | 108 +++++++++++++++++++++ reference/generate_all_aln2fa.html | 19 +--- reference/index.html | 48 +++++++++- reference/mapAcc2Name.html | 85 +++++++++++++++++ reference/map_acc2name.html | 11 +-- reference/renameFA.html | 84 ++++++++++++++++ reference/rename_fasta.html | 11 +-- reference/to_title.html | 4 +- reference/to_titlecase.html | 18 ++-- reference/totitle,.html | 4 +- search.json | 2 +- sitemap.xml | 7 ++ 22 files changed, 796 insertions(+), 136 deletions(-) create mode 100644 reference/addLeaves2Alignment.html create mode 100644 reference/addName.html create mode 100644 reference/convert2TitleCase.html create mode 100644 reference/convertAlignment2FA.html create mode 100644 reference/generateAllAlignments2FA.html create mode 100644 reference/mapAcc2Name.html create mode 100644 reference/renameFA.html diff --git a/pkgdown.yml b/pkgdown.yml index 53a03492..45a50061 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -2,7 +2,7 @@ pandoc: 3.1.11 pkgdown: 2.1.1 pkgdown_sha: ~ articles: {} -last_built: 2024-09-20T14:19Z +last_built: 2024-10-07T20:12Z urls: reference: https://jravilab.github.io/MolEvolvR/reference article: https://jravilab.github.io/MolEvolvR/articles diff --git a/reference/acc2fa.html b/reference/acc2fa.html index 243c2b97..d54f807c 100644 --- a/reference/acc2fa.html +++ b/reference/acc2fa.html @@ -1,8 +1,6 @@ -acc2fa converts protein accession numbers to a fasta format. — acc2fa • MolEvolvRacc2fa — acc2fa • MolEvolvR Skip to contents @@ -31,22 +29,19 @@
-

acc2fa converts protein accession numbers to a fasta format.

- Source: R/CHANGED-pre-msa-tree.R, R/pre-msa-tree.R +

acc2fa

+ Source: R/pre-msa-tree.R
acc2fa.Rd
-

Resulting fasta file is written to the outpath.

-

acc2fa converts protein accession numbers to a fasta format. +

acc2fa converts protein accession numbers to a fasta format. Resulting fasta file is written to the outpath.

Usage

- 
acc2fa(accessions, outpath, plan = "sequential")
-
-acc2fa(accessions, outpath, plan = "sequential")
+ 
acc2fa(accessions, outpath, plan = "sequential")
@@ -78,11 +73,6 @@

ExamplesEntrez:accessions <- rep("ANY95992.1", 201) |> acc2fa(outpath = "entrez.fa") EBI:accessions <- c("P12345", "Q9UHC1", "O15530", "Q14624", "P0DTD1") |> acc2fa(outpath = "ebi.fa") } # } -if (FALSE) { # \dontrun{ -acc2fa(accessions = c("ACU53894.1", "APJ14606.1", "ABK37082.1"), outpath = "my_proteins.fasta") -Entrez:accessions <- rep("ANY95992.1", 201) |> acc2fa(outpath = "entrez.fa") -EBI:accessions <- c("P12345", "Q9UHC1", "O15530", "Q14624", "P0DTD1") |> acc2fa(outpath = "ebi.fa") -} # }