Add .bed documentation

nvelden · Apr 26, 2024 · 0055d86 · 0055d86
1 parent 94b7178
commit 0055d86
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Showing 14 changed files with 290 additions and 160 deletions.
diff --git a/R/read_genbank.R b/R/read_genbank.R
@@ -55,12 +55,12 @@ read_gbk <- function(path, sections = NULL, features = NULL, origin = TRUE) {
     }
 
     # Process each .gbk file in the directory
-    basename <- sapply(files, function(x) sub("\\.gbk$", "", basename(x)))
+    basename <- sapply(files, function(x) sub("\\.gbk$|\\.gb$", "", basename(x)))
     results <- setNames(lapply(files, function(file) process_gbk(file, sections, features, origin, basename(file))),
                         basename)
 
   } else if (file.exists(path)) {
-    basename <- sub("\\.gbk$", "", basename(path))
+    basename <- sub("\\.gbk$|\\.gb$", "", basename(path))
     results[[basename]] <- process_gbk(path, sections, features, origin, basename)
   } else {
     stop("The specified path does not exist.")

diff --git a/README.md b/README.md
@@ -1,9 +1,6 @@
 <p align="center">
-
-<img src="man/figures/logo.png" class="pkgdown-hide" height="150px" align="right"/>
-
-<h1><strong>geneviewer</strong> - Gene Cluster Visualizations in R</h1>
-
+  <img src="man/figures/logo.png" class="pkgdown-hide" height="150px" align="right">
+  <h1><strong>geneviewer</strong> - Gene Cluster Visualizations in R</h1>
 </p>
 
 <!-- badges: start -->
@@ -14,7 +11,7 @@
 
 ## geneviewer
 
-**geneviewer** is an R package designed for visualizing gene clusters. It can import data directly from GenBank, GFF and FASTA files, perform BlastP alignments between clusters and visualize the results in gene arrow maps. In addition there are extensive options to customize the gene arrow maps such as adding a legend, labels, links, annotations, customized scales, colors, tooltips and much more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html).
+**geneviewer** is an R package designed for visualizing gene clusters. It can import data directly from GenBank, GFF, BED and FASTA files, perform BlastP alignments between clusters and visualize the results in gene arrow maps. In addition there are extensive options to customize the gene arrow maps such as adding a legend, labels, links, annotations, customized scales, colors, tooltips and much more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html).
 
 ## Installation
 

diff --git a/docs/articles/BLASTP.html b/docs/articles/BLASTP.html
diff --git a/docs/articles/Examples.html b/docs/articles/Examples.html
diff --git a/docs/articles/LoadFastaFiles.html b/docs/articles/LoadFastaFiles.html
diff --git a/docs/articles/LoadGFF.html b/docs/articles/LoadGFF.html
diff --git a/docs/articles/LoadGenBankFiles.html b/docs/articles/LoadGenBankFiles.html
diff --git a/docs/articles/geneviewer.html b/docs/articles/geneviewer.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   LoadGFF: LoadGFF.html
   LoadGenBankFiles: LoadGenBankFiles.html
   geneviewer: geneviewer.html
-last_built: 2024-04-25T14:04Z
+last_built: 2024-04-26T13:40Z
 urls:
   reference: https://nvelden.github.io/geneviewer/reference
   article: https://nvelden.github.io/geneviewer/articles

diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/read_bed.html b/docs/reference/read_bed.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -135,6 +135,9 @@
   <url>
     <loc>https://nvelden.github.io/geneviewer/reference/protein_blast.html</loc>
   </url>
+  <url>
+    <loc>https://nvelden.github.io/geneviewer/reference/read_bed.html</loc>
+  </url>
   <url>
     <loc>https://nvelden.github.io/geneviewer/reference/read_fasta.html</loc>
   </url>
-Original file line number
+Diff line change
@@ Expand Up / @@ -135,6 +135,9 @@ @@
       <url>
         <loc>https://nvelden.github.io/geneviewer/reference/protein_blast.html</loc>
       </url>
+      <url>
+        <loc>https://nvelden.github.io/geneviewer/reference/read_bed.html</loc>
+      </url>
       <url>
         <loc>https://nvelden.github.io/geneviewer/reference/read_fasta.html</loc>
       </url>
@@ Expand Down @@