03/06: gnu: Add r-structstrings.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 5c10649a50dd91f5ece816d949e4a751e8ba3777
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Jan 19 23:40:14 2024 +0100

    gnu: Add r-structstrings.
    
    * gnu/packages/bioconductor.scm (r-structstrings): New variable.
    
    Change-Id: I9759520a03ee8178432591c48bf56fb25a379f27
---
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5e7dcfd1f2..d46c86db13 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11400,6 +11400,40 @@ associations.  Each interaction is associated with a 
combined confidence score
 that integrates the various evidences.")
     (license license:gpl2)))
 
+(define-public r-structstrings
+  (package
+    (name "r-structstrings")
+    (version "1.18.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Structstrings" version))
+       (sha256
+        (base32 "10j1khhjd30wn9yfz4jhgx34z0yyijgwgydr8ric52337vwpx6dl"))))
+    (properties `((upstream-name . "Structstrings")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocgenerics
+                             r-biostrings
+                             r-crayon
+                             r-iranges
+                             r-s4vectors
+                             r-stringi
+                             r-stringr
+                             r-xvector))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/FelixErnst/Structstrings";)
+    (synopsis "Implementation of the dot bracket annotations with Biostrings")
+    (description
+     "The Structstrings package implements the widely used dot bracket
+annotation for storing base pairing information in structured
+RNA. Structstrings uses the infrastructure provided by the Biostrings package
+and derives the @code{DotBracketString} and related classes from the BString
+class.  From these, base pair tables can be produced for in depth analysis.
+In addition, the loop indices of the base pairs can be retrieved as well.  For
+better efficiency, information conversion is implemented in C, inspired to a
+large extend by the @code{ViennaRNA} package.")
+    (license license:artistic2.0)))
+
 (define-public r-structuralvariantannotation
   (package
     (name "r-structuralvariantannotation")