1 files changed, 52 insertions(+), 0 deletions(-)

M gnu/packages/bioinformatics.scm

@@ 98,6 98,7 @@
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
+  #:use-module (gnu packages ghostscript)
   #:use-module (gnu packages golang)
   #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)


@@ 3224,6 3225,57 @@ matplotlib Axes objects, making them easy to style and incorporate into
 multi-panel figures.")
     (license license:expat)))
 
+(define-public python-weblogo
+  (package
+    (name "python-weblogo")
+    (version "3.7.12")
+    (home-page "https://github.com/gecrooks/weblogo")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "weblogo" version))
+       (sha256
+        (base32
+         "0mw6aa0dq3kk9k1nakdvm64icz9504spqbvq4v2h0rb1cb52frkw"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list ghostscript
+                             python-numpy
+                             python-pluggy
+                             python-scipy))
+    (native-inputs (list ghostscript
+                         python-importlib-metadata
+                         python-importlib-resources
+                         python-pytest
+                         python-setuptools
+                         python-setuptools-scm
+                         python-wheel))
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             ;; These tests fail because of circular imports
+             (string-append "not test_cli.py"
+                            " and not test_transformseq.py"))))
+    (synopsis "Sequence Logo Generator")
+    (description "WebLogo is a web based application designed to make the
+generation of sequence logos as easy and painless as possible.
+
+WebLogo can create output in several common graphics' formats, including the
+bitmap formats GIF and PNG, suitable for on-screen display, and the vector
+formats EPS and PDF, more suitable for printing, publication, and further
+editing.  Additional graphics options include bitmap resolution, titles,
+optional axis, and axis labels, antialiasing, error bars, and alternative
+symbol formats.
+
+A sequence logo is a graphical representation of an amino acid or nucleic acid
+multiple sequence alignment.  Each logo consists of stacks of symbols, one
+stack for each position in the sequence.  The overall height of the stack
+indicates the sequence conservation at that position, while the height of
+symbols within the stack indicates the relative frequency of each amino or
+nucleic acid at that position.  The width of the stack is proportional to the
+fraction of valid symbols in that position.")
+    (license license:expat)))
+
 (define-public python-magic-impute
   (package
     (name "python-magic-impute")