Metadata-Version: 1.1
Name: NanoComp
Version: 0.7.0
Summary: Comparing runs of Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoComp
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: NanoComp
        ========
        
        Compare multiple runs of Oxford Nanopore sequencing data and alignments
        
        |Twitter URL| |Build Status|
        
        INSTALLATION
        ~~~~~~~~~~~~
        
        ``pip install NanoComp``
        
        This script is written for Python3.
        
        USAGE
        ~~~~~
        
        ::
        
            NanoComp [-h] [-v] [-t THREADS] [--readtype {1D,2D,1D2}] [-o OUTDIR]
                            [-p PREFIX]
                            [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                            [-n [NAMES [NAMES ...]]]
                            (--fastq [FASTQ [FASTQ ...]] | --summary [SUMMARY [SUMMARY ...]] | --bam [BAM [BAM ...]])
        
        
            optional arguments:
              -h, --help            show this help message and exit
              -v, --version         Print version and exit.
              -t, --threads THREADS Set the allowed number of threads to be used by the script
              --readtype {1D,2D,1D2}
                                    Which read type to extract information about from
                                    summary. Options are 1D, 2D, 1D2
              -o, --outdir OUTDIR   Specify directory in which output has to be created.
              -p, --prefix PREFIX   Specify an optional prefix to be used for the output
                                    files.
              -f, --format {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}
                                    Specify the output format of the plots.
              -n, --names [NAMES [NAMES ...]]
                                    Specify the names to be used for the datasets
              --plot {violin,box}   Which plot type to use: boxplot or violinplot (default)
              --fastq [FASTQ [FASTQ ...]]
                                    Data is in default fastq format.
              --summary [SUMMARY [SUMMARY ...]]
                                    Data is a summary file generated by albacore.
              --bam [BAM [BAM ...]]
                                    Data as a sorted bam file.
        
        EXAMPLES
        ~~~~~~~~
        
        ::
        
            NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs
            NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 run3 run4
        
        EXAMPLE OUTPUT
        ~~~~~~~~~~~~~~
        
        |loglength example| |box percentIdentity example|
        
        `See more
        examples <https://github.com/wdecoster/nanocomp/tree/master/examples>`__
        
        I welcome all suggestions, bug reports, feature requests and
        contributions. Please leave an
        `issue <https://github.com/wdecoster/nanocomp/issues>`__ or open a pull
        request. I will usually respond within a day, or rarely within a few
        days.
        
        .. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
           :target: https://twitter.com/wouter_decoster
        .. |Build Status| image:: https://travis-ci.org/wdecoster/nanocomp.svg?branch=master
           :target: https://travis-ci.org/wdecoster/nanocomp
        .. |loglength example| image:: https://github.com/wdecoster/nanocomp/blob/master/examples/NanoComp_log_length.png
        .. |box percentIdentity example| image:: https://github.com/wdecoster/nanocomp/blob/master/examples/box_NanoComp_percentIdentity.png
        
        
Keywords: nanopore sequencing plotting quality control
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
