.. _`bio/liftoff`: LIFTOFF ======= .. image:: https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/liftoff?label=version%20update%20pull%20requests :target: https://github.com/snakemake/snakemake-wrappers/pulls?q=is%3Apr+is%3Aopen+label%3Abio/liftoff Lift features from one genome assembly to another **URL**: https://github.com/agshumate/Liftoff Example ------- This wrapper can be used in the following way: .. code-block:: python rule liftoff: input: ref="{ref}.fasta.gz", tgt="{tgt}.fasta.gz", ann="{ann}.gff.gz", output: main="{ref}_{ann}_{tgt}.gff3", unmapped="{ref}_{ann}_{tgt}.unmapped.txt", log: "logs/liftoff_{ref}_{ann}_{tgt}.log", params: extra="", threads: 1 wrapper: "v5.7.0/bio/liftoff" Note that input, output and log file paths can be chosen freely. When running with .. code-block:: bash snakemake --use-conda the software dependencies will be automatically deployed into an isolated environment before execution. Software dependencies --------------------- * ``liftoff=1.6.3`` Input/Output ------------ **Input:** * A fasta formatted reference genome file * A fasta formatted target genome file * A GFF/GTF formatted annotations file **Output:** * A GFF formatted file containing the mapped annotations * A GFF formatted file containing the unmapped annotations Authors ------- * Tomás Di Domenico Code ---- .. code-block:: python """Snakemake wrapper for liftoff""" __author__ = "Tomás Di Domenico" __copyright__ = "Copyright 2021, Tomás Di Domenico" __email__ = "tdido@tdido.ar" __license__ = "MIT" from snakemake.shell import shell log = snakemake.log_fmt_shell(stdout=True, stderr=True) extra = snakemake.params.get("extra", "") shell( "liftoff " # tool "-g {snakemake.input.ann} " # annotation file to lift over in GFF or GTF format "-o {snakemake.output.main} " # main output "-u {snakemake.output.unmapped} " # unmapped output "{extra} " # optional parameters "{snakemake.input.tgt} " # target fasta genome to lift genes to "{snakemake.input.ref} " # reference fasta genome to lift genes from "{log}" # Logging ) .. |nl| raw:: html