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-rw-r--r--blist-stopiteration.patch36
-rw-r--r--gn/packages/bioinformatics.scm80
2 files changed, 116 insertions, 0 deletions
diff --git a/blist-stopiteration.patch b/blist-stopiteration.patch
new file mode 100644
index 0000000..198bef4
--- /dev/null
+++ b/blist-stopiteration.patch
@@ -0,0 +1,36 @@
+From: Andrej Shadura <andrew.shadura@collabora.co.uk>
+Date: Sun, 8 Jul 2018 09:00:16 +0200
+Subject: Catch StopIteration in a generator and return instead, per PEP 479
+
+Signed-off-by: Andrej Shadura <andrew.shadura@collabora.co.uk>
+
+Forwarded: https://github.com/DanielStutzbach/blist/pull/92
+Bug-Debian: https://bugs.debian.org/902757
+---
+ blist/_sortedlist.py | 13 ++++++++-----
+ 1 file changed, 8 insertions(+), 5 deletions(-)
+
+diff --git a/blist/_sortedlist.py b/blist/_sortedlist.py
+index b34f69e..1f77170 100644
+--- a/blist/_sortedlist.py
++++ b/blist/_sortedlist.py
+@@ -420,11 +420,14 @@ class _setmixin(object):
+ def __iter__(self):
+ it = super(_setmixin, self).__iter__()
+ while True:
+- item = next(it)
+- n = len(self)
+- yield item
+- if n != len(self):
+- raise RuntimeError('Set changed size during iteration')
++ try:
++ item = next(it)
++ n = len(self)
++ yield item
++ if n != len(self):
++ raise RuntimeError('Set changed size during iteration')
++ except StopIteration:
++ return
+
+ def safe_cmp(f):
+ def g(self, other):
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8d4edaa..391c2bf 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,6 +10,7 @@
#:use-module (guix build-system ant)
#:use-module (guix build-system cargo)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (guix build-system python)
@@ -2805,3 +2806,82 @@ including @acronym{TIPP, taxonomic identical using phylogenetic placement} and
(description "Assess genome assembly and annotation completeness with
Benchmarking Universal Single-Copy Orthologs.")
(license license:expat)))
+
+(define-public mutation-simulator
+ (let ((commit "9cb6bd2acf8201151bc610be14963e65b41d8899") ; March 25, 2021
+ (revision "1"))
+ (package
+ (name "mutation-simulator")
+ (version (git-version "2.0.3" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mkpython3/mutation-simulator")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1yxn5v5x804rm5ra1srmnph468yk7amsgfsj6h20rd6nmj2j0g9c"))))
+ (build-system copy-build-system)
+ (arguments
+ `(#:install-plan
+ '(("mutation-simulator.py" "bin/"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'wrap-script
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (script (string-append out "/bin/mutation-simulator.py")))
+ ;; wrap-script doesn't accept arguments
+ (wrap-program script
+ `("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH"))))
+ (chmod script #o555)
+ ;; When using wrap-script.
+ (when (file-exists?
+ (string-append out "/bin/.mutation-simulator.py-real"))
+ (chmod (string-append out "/bin/.mutation-simulator.py-real")
+ #o555))
+ #t)))
+ (add-after 'wrap-script 'check
+ (lambda* (#:key tests? outputs #:allow-other-keys)
+ (when tests?
+ (invoke (string-append (assoc-ref outputs "out")
+ "/bin/mutation-simulator.py")
+ "Test/test.fa" "rmt" "Test/test.rmt")))))))
+ (inputs
+ `(("bash" ,bash-minimal) ; for wrap-program
+ ;("guile" ,(@ (gnu packages guile) guile-3.0)) ; for wrap-script
+ ("python" ,python)
+ ("python-blist" ,python-blist)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-numpy" ,python-numpy)
+ ("python-tqdm" ,python-tqdm)))
+ (home-page "https://github.com/mkpython3/mutation-simulator")
+ (synopsis "Simulate mutations on given fasta files")
+ (description "Mutation-Simulator is a Python tool for simulating SNPs and
+SVs in any reference genome with cohesive documentation about implemented
+mutations. With Mutation-Simulator, the new file format @acronym{RMT, Random
+Mutation Tables} is introduced, which gives more simulation power to the user by
+creating an interface for more natural simulations within specific genomes.
+Mutation-Simulator provides 3 different modes to simulate SNPs, insertions,
+deletions, tandem duplications, inversions, translocations and interchromosomal
+translocations from the commandline or with highly configureable RMT files.")
+ (license license:gpl3+))))
+
+(define-public python-blist
+ (package
+ (name "python-blist")
+ (version "1.3.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "blist" version))
+ (sha256
+ (base32 "1hqz9pqbwx0czvq9bjdqjqh5bwfksva1is0anfazig81n18c84is"))
+ (patches (search-patches "blist-stopiteration.patch"))))
+ (build-system python-build-system)
+ (home-page "http://stutzbachenterprises.com/blist/")
+ (synopsis "List-like type for Python with better asymptotic performance")
+ (description
+ "This package provides a list-like type for Python with better asymptotic
+performance and similar performance on small lists.")
+ (license license:bsd-3)))