From cb15b360aabb9a572dd8f4a697e50cba4481902e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 5 Jan 2024 17:55:17 +0100
Subject: gnu: Add python-snaptools.

* gnu/packages/bioinformatics.scm (python-snaptools): New variable.

Change-Id: I4f4b32cbbb64472e65d2d88184173b6e1a75e8d2
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4bed2e4fe8..a363298386 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2366,6 +2366,40 @@ (define-public python-scdamandtools
 counts.")
     (license license:expat)))
 
+(define-public python-snaptools
+  (package
+    (name "python-snaptools")
+    (version "1.4.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "snaptools" version))
+       (sha256
+        (base32
+         "1s5373g5jjbshh3q39zy7dlxr7nda6ksxq9d1gw46h82c4fsmfbn"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (list python-future
+           python-h5py
+           python-louvain
+           python-numpy
+           python-pybedtools
+           python-pysam))
+    (home-page "https://github.com/r3fang/SnapTools")
+    (synopsis "Tools for processing snap files" )
+    (description
+     "@code{SnapTools} can operate on snap files the following types of
+operations:
+
+@itemize
+@item index the reference genome before alignment;
+@item align reads to the corresponding reference genome;
+@item pre-process by convert pair-end reads into fragments, checking the
+  mapping quality score, alingment and filtration;
+@item create the cell-by-bin matrix.
+@end itemize")
+    (license license:asl2.0)))
+
 (define-public python-bioframe
   (package
     (name "python-bioframe")
-- 
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