02/02: gnu: Add python-goatools.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 5daf470e4fa4d16486d32c767e8d5e257cefebf6
Author: Navid Afkhami <navid.afkhami@mdc-berlin.de>
AuthorDate: Thu May 4 14:56:49 2023 +0000

    gnu: Add python-goatools.
    
    * gnu/packages/bioinformatics.scm (python-goatools): New variable.
    
    Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
---
 gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7db8a91e80..7ee97e3da5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12337,6 +12337,48 @@ selection of file types and formats for handling 
genomic region data---all
 using the same syntax.")
     (license license:expat)))
 
+(define-public python-goatools
+  (package
+    (name "python-goatools")
+    (version "1.3.1")
+    ;; Pypi tarball doesn't include test files.
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/tanghaibao/goatools";)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0a295zk9jc8kny5vnka63q3gbksins42kcmgvskf8xy7hkca7cmq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Almost all tests require access to the internet.
+      #:tests? #false
+      #:test-flags
+      ;; These have syntax errors.
+      '(list "--ignore=tests/test_i195_sgd_gaf.py"
+             "--ignore=tests/test_i206.py"
+             "--ignore=tests/test_setup_dirs.py")))
+    (propagated-inputs (list python-docopt
+                             python-numpy
+                             python-openpyxl
+                             python-pandas
+                             python-pydot
+                             python-requests
+                             python-scipy
+                             python-statsmodels
+                             python-xlsxwriter))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/tanghaibao/goatools";)
+    (synopsis "Python scripts to find enrichment of GO terms")
+    (description "Python scripts to find enrichment of GO terms.  In addition,
+this package is used for processing the obo-formatted file from Gene Ontology
+website.  The data structure is a directed acyclic graph that allows easy
+traversal from leaf to root.")
+    (license license:bsd-2)))
+
 (define-public python-loompy
   (package
     (name "python-loompy")