{
    "info": {
        "author": "Sung-Huan Yu",
        "author_email": "sung-huan.yu@uni-wuerzburg.de",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: ISC License (ISCL)",
            "Operating System :: POSIX",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": ".. image:: https://img.shields.io/pypi/v/annogesic.svg\n   :target: https://pypi.python.org/pypi/ANNOgesic/\n.. image:: https://img.shields.io/pypi/l/annogesic.svg\n   :target: https://pypi.python.org/pypi/ANNOgesic/\n.. image:: https://zenodo.org/badge/34061246.svg\n   :target: https://zenodo.org/badge/latestdoi/34061246\n\nAbout ANNOgesic\n---------------\n\nANNOgesic is the swiss army knife for RNA-Seq based annotation of\nbacterial/archaeal genomes.\n\nIt is a modular, command-line tool that can integrate different types\nof RNA-Seq data based on dRNA-Seq (differential RNA-Seq) or RNA-Seq\nprotocols that inclusde transcript fragmentation to generate high\nquality genome annotations. It can detect genes, CDSs/tRNAs/rRNAs,\ntranscription starting sites (TSS) and processing sites, transcripts,\nterminators, untranslated regions (UTR) as well as small RNAs (sRNA),\nsmall open reading frames (sORF), circular RNAs, CRISPR related RNAs,\nriboswitches and RNA-thermometers. It can also perform RNA-RNA and\nprotein-protein interactions prediction. Furthermore, it groups genes\ninto operons and sub-operons and reveal promoter motifs. It can also\nallocate GO term and subcellular localization to genes. Several of\nANNOgesic features are new implementations while other build on well\nknown third-party tools for which it offers adaptive\nparameter-optimizations. Additionally, numerous visualization and\nstatistics help the user to quickly evaluat feature predictions\nresulting from an ANNOgesic analysis. The tool was heavily tested\nwith several RNA-Seq data set from bacterial as well as archaeal\nsamples.\n\nDocumentation\n-------------\n\nDocumentation can be found on\n`here <http://annogesic.readthedocs.io/en/latest/index.html>`__.\n\nInstallation\n------------\n\nPip3\n^^^^\n\nIf you have all the requirements installed, installation can be done by \nusing pip3.\n\nWith root permission: \n\n::\n\n    $ pip3 install ANNOgesic\n\nwithout root permission\n\n::\n\n    $ pip3 install --user ANNOgesic\n\nIf you want to know the requirement, please refer to \n`Documentation <http://annogesic.readthedocs.io/en/latest/index.html>`__.\n\nDocker and Singularity\n^^^^^^^^^^^^^^^^^^^^^^\n\nIn order to solve the issue of installing the dependencies, a Docker image of ANNOgesic is provided in \n`Docker Hub <https://hub.docker.com/r/silasysh/annogesic/>`__. \nThe image can be pulled by using `Docker <https://www.docker.com/>`__ or `Singularity <https://singularity.lbl.gov/index.html>`__. \nMoreover, the users can build an Docker image from the `Dockerfile <https://github.com/Sung-Huan/ANNOgesic>`__ by themselves. \nFor the details, please check the `documentation <http://annogesic.readthedocs.io/en/latest/installation.html>`__.\n\nGithub\n^^^^^^\n\nThe alternative way for installing ANNOgesic is directly clone the Git repository.\n\n::\n\n    $ git clone https://github.com/Sung-Huan/ANNOgesic.git\n\nor\n\n::\n\n    $ git clone git@github.com:Sung-Huan/ANNOgesic.git\n\nIn order to make ANNOgesic runnable, we should create a soft link of ``annogesiclib`` in ``bin``.\n\n::\n\n    $ cd ANNOgesic/bin\n    $ ln -s ../annogesiclib .\n\nThen, you can run ANNOgesic via specifying the installed path if all the requirements are setup properly.\n\nArguments\n-------------\n\n::\n\n    usage: annogesic [-h] [--version]\n                     {create,get_input_files,update_genome_fasta,annotation_transfer,\n                      tss_ps,optimize_tss_ps,terminator,transcript,utr,srna,sorf,\n                      promoter,operon,circrna,go_term,srna_target,snp,ppi_network,\n                      localization,riboswitch_thermometer,crispr,merge_features,\n                      screenshot,colorize_screenshot_tracks}\n                     ...\n\n    positional arguments:\n      {create,get_input_files,update_genome_fasta,annotation_transfer,tss_ps,\n       optimize_tss_ps,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,\n       go_term,srna_target,snp,ppi_network,localization,riboswitch_thermometer,\n       crispr,merge_features,screenshot,colorize_screenshot_tracks}\n                            commands\n        create              Create a project\n        get_input_files     Get required files. (i.e. annotation files, fasta\n                            files)\n        update_genome_fasta\n                            Get fasta files of query genomes if the query\n                            sequences do not exist.\n        annotation_transfer\n                            Transfer the annotations from a closely related\n                            species genome to a target genome.\n        tss_ps              Detect TSSs or processing sites.\n        optimize_tss_ps     Optimize TSSs or processing sites based on manual\n                            detected ones.\n        terminator          Detect rho-independent terminators.\n        transcript          Detect transcripts based on coverage file.\n        utr                 Detect 5'UTRs and 3'UTRs.\n        srna                Detect intergenic, antisense and UTR-derived sRNAs.\n        sorf                Detect expressed sORFs.\n        promoter            Discover promoter motifs.\n        operon              Detect operons and sub-operons.\n        circrna             Detect circular RNAs.\n        go_term             Extract GO terms from Uniprot.\n        srna_target         Detect sRNA-mRNA interactions.\n        snp                 Detect SNP/mutation and generate fasta file if\n                            mutations were found.\n        ppi_network         Detect protein-protein interactions suported by\n                            literature.\n        localization        Predict subcellular localization of proteins.\n        riboswitch_thermometer\n                            Predict riboswitches and RNA thermometers.\n        crispr              Predict CRISPR related RNAs.\n        merge_features      Merge all features to one gff file.\n        screenshot          Generate screenshots for selected features using IGV.\n        colorize_screenshot_tracks\n                            Add color information to screenshots (e.g. useful for\n                            dRNA-Seq based TSS and PS detection. It only works\n                            after running \"screenshot\" (after running batch\n                            script).\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --version, -v         show version\n\nCitation\n--------\n\nSH Yu, J. Vogel, KU F\u00f6rstner. 2018, GigaScience,\n`DOI:10.1093/gigascience/giy096 <https://academic.oup.com/gigascience/advance-article/doi/10.1093/gigascience/giy096/5087959>`_,\n`PMID:30169674 <https://www.ncbi.nlm.nih.gov/pubmed/30169674>`_.\n\n\nLicense\n-------\n\n`ISC <https://en.wikipedia.org/wiki/ISC_license>`__ (Internet Systems\nConsortium license ~ simplified BSD license) - see `LICENSE <http://annogesic.readthedocs.io/en/latest/license.html>`__\n\nContact\n-------\n\nIf you have any questions, please contact `Sung-Huan Yu <mailto:shyu@biochem.mpg.de>`_\n\n\n",
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        "name": "ANNOgesic",
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