Metadata-Version: 1.1
Name: ANNOgesic
Version: 0.7.14
Summary: ANNOgesic - A tool for bacterial/archaeal RNA-Seq based genome annotations
Home-page: https://github.com/Sung-Huan/ANNOgesic
Author: Sung-Huan Yu
Author-email: sung-huan.yu@uni-wuerzburg.de
License: ISC License (ISCL)
Description: .. image:: https://img.shields.io/pypi/v/annogesic.svg
           :target: https://pypi.python.org/pypi/ANNOgesic/
        .. image:: https://img.shields.io/pypi/l/annogesic.svg
           :target: https://pypi.python.org/pypi/ANNOgesic/
        .. image:: https://zenodo.org/badge/34061246.svg
           :target: https://zenodo.org/badge/latestdoi/34061246
        
        About ANNOgesic
        ---------------
        
        ANNOgesic is the swiss army knife for RNA-Seq based annotation of
        bacterial/archaeal genomes.
        
        It is a modular, command-line tool that can integrate different types
        of RNA-Seq data based on dRNA-Seq (differential RNA-Seq) or RNA-Seq
        protocols that inclusde transcript fragmentation to generate high
        quality genome annotations. It can detect genes, CDSs/tRNAs/rRNAs,
        transcription starting sites (TSS) and processing sites, transcripts,
        terminators, untranslated regions (UTR) as well as small RNAs (sRNA),
        small open reading frames (sORF), circular RNAs, CRISPR related RNAs,
        riboswitches and RNA-thermometers. It can also perform RNA-RNA and
        protein-protein interactions prediction. Furthermore, it groups genes
        into operons and sub-operons and reveal promoter motifs. It can also
        allocate GO term and subcellular localization to genes. Several of
        ANNOgesic features are new implementations while other build on well
        known third-party tools for which it offers adaptive
        parameter-optimizations. Additionally, numerous visualization and
        statistics help the user to quickly evaluat feature predictions
        resulting from an ANNOgesic analysis. The tool was heavily tested
        with several RNA-Seq data set from bacterial as well as archaeal
        samples.
        
        Documentation
        -------------
        
        Documentation can be found on
        `here <http://annogesic.readthedocs.io/en/latest/index.html>`__.
        
        Installation
        ------------
        
        Short version (if you have all the requirements installed):
        
        ::
        
            $ pip3 install ANNOgesic
        
        If you want to know the requirement, please refer to 
        `Documentation <http://annogesic.readthedocs.io/en/latest/index.html>`__.
        
        Arguments
        -------------
        
        ::
        
            usage: annogesic [-h] [--version]
                             {create,get_input_files,update_genome_fasta,annotation_transfer,
                              tss_ps,optimize_tss_ps,terminator,transcript,utr,srna,sorf,
                              promoter,operon,circrna,go_term,srna_target,snp,ppi_network,
                              localization,riboswitch_thermometer,crispr,merge_features,
                              screenshot,colorize_screenshot_tracks}
                             ...
            
            positional arguments:
              {create,get_input_files,update_genome_fasta,annotation_transfer,tss_ps,
               optimize_tss_ps,terminator,transcript,utr,srna,sorf,promoter,operon,circrna,
               go_term,srna_target,snp,ppi_network,localization,riboswitch_thermometer,
               crispr,merge_features,screenshot,colorize_screenshot_tracks}
                                    commands
                create              Create a project
                get_input_files     Get required files. (i.e. annotation files, fasta
                                    files)
                update_genome_fasta
                                    Get fasta files of query genomes if the query
                                    sequences do not exist.
                annotation_transfer
                                    Transfer the annotations from a closely related
                                    species genome to a target genome.
                tss_ps              Detect TSSs or processing sites.
                optimize_tss_ps     Optimize TSSs or processing sites based on manual
                                    detected ones.
                terminator          Detect rho-independent terminators.
                transcript          Detect transcripts based on coverage file.
                utr                 Detect 5'UTRs and 3'UTRs.
                srna                Detect intergenic, antisense and UTR-derived sRNAs.
                sorf                Detect expressed sORFs.
                promoter            Discover promoter motifs.
                operon              Detect operons and sub-operons.
                circrna             Detect circular RNAs.
                go_term             Extract GO terms from Uniprot.
                srna_target         Detect sRNA-mRNA interactions.
                snp                 Detect SNP/mutation and generate fasta file if
                                    mutations were found.
                ppi_network         Detect protein-protein interactions suported by
                                    literature.
                localization        Predict subcellular localization of proteins.
                riboswitch_thermometer
                                    Predict riboswitches and RNA thermometers.
                crispr              Predict CRISPR related RNAs.
                merge_features      Merge all features to one gff file.
                screenshot          Generate screenshots for selected features using IGV.
                colorize_screenshot_tracks
                                    Add color information to screenshots (e.g. useful for
                                    dRNA-Seq based TSS and PS detection. It only works
                                    after running "screenshot" (after running batch
                                    script).
            
            optional arguments:
              -h, --help            show this help message and exit
              --version, -v         show version
        
        License
        -------
        
        `ISC <https://en.wikipedia.org/wiki/ISC_license>`__ (Internet Systems
        Consortium license ~ simplified BSD license) - see `LICENSE <http://annogesic.readthedocs.io/en/latest/license.html>`__
        
        Contact
        -------
        
        If you have any questions, please contact `Sung-Huan Yu <mailto:sung-huan.yu@uni-wuerzburg.de>`_
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: ISC License (ISCL)
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
