diff options
| -rw-r--r-- | blist-stopiteration.patch | 36 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 80 |
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))) |