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| -rw-r--r-- | gn/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 3734a79..a404c7b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -4973,3 +4973,61 @@ today's most advanced CPUs.") (description "This package provides Python bindings for the parasail C library.") (license license:bsd-2))) + +(define-public liftoff + (package + (name "liftoff") + (version "1.6.3") + (source + ;; The PyPI tarball is missing the tests. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/agshumate/Liftoff") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "18840vdv75nsq0fw5hzvrp7l0k6ciamlzkhgxxhnjh23ghih71dx")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-version-requirements + (lambda _ + (substitute* "setup.py" + (("==") ">="))))))) + (inputs + (list python-biopython + python-gffutils + python-interlap + python-networkx + python-numpy + python-parasail + python-pyfaidx + python-pysam + python-ujson)) + (native-inputs + (list minimap2 + python-pytest + python-setuptools + python-wheel)) + (home-page "https://github.com/ashumate/Liftoff") + (synopsis "GFF3/GTF lift over pipeline") + (description "Liftoff is a tool that accurately maps annotations +in GFF or GTF between assemblies of the same, or closely-related +species. Unlike current coordinate lift-over tools which require a +pre-generated “chain” file as input, Liftoff is a standalone tool that +takes two genome assemblies and a reference annotation as input and +outputs an annotation of the target genome. Liftoff uses minimap2 to +align the gene sequences from a reference genome to the target genome. +Rather than aligning whole genomes, aligning only the gene sequences +allows genes to be lifted over even if there are many structural +differences between the two genomes. For each gene, Liftoff finds the +alignments of the exons that maximize sequence identity while +preserving the transcript and gene structure. If two genes incorrectly +map to overlapping loci, Liftoff determines which gene is most-likely +mis-mapped, and attempts to re-map it. Liftoff can also find +additional gene copies present in the target assembly that are not +annotated in the reference.") + (license license:gpl3+))) |