Metadata-Version: 1.2
Name: NanoPlot
Version: 1.9.2
Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
Home-page: https://github.com/wdecoster/NanoPlot
Author: Wouter De Coster
Author-email: decosterwouter@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: NanoPlot
        ========
        
        Plotting tool for long read sequencing data and alignments.
        
        |Twitter URL| |conda badge| |Build Status| |Code Health|
        
        .. figure:: https://github.com/wdecoster/NanoPlot/blob/master/examples/scaled_Log_Downsampled_LengthvsQualityScatterPlot_kde.png
           :alt: Example plot
        
           Example plot
        
        The example plot above shows a bivariate plot comparing log transformed
        read length with average basecall Phred quality score. More examples can
        be found in the `gallery on my blog 'Gigabase Or
        Gigabyte'. <https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/>`__
        
        In addition to various plots also a NanoStats file is created
        summarizing key features of the dataset.
        
        | This script performs data extraction from Oxford Nanopore sequencing
          data in the following formats:
        | - fastq files
        | (can be bgzip, bzip2 or gzip compressed)
        | - fastq files generated by albacore or MinKNOW containing additional
          information
        | (can be bgzip, bzip2 or gzip compressed)
        | - sorted bam files
        | - sequencing\_summary.txt output table generated by albacore
        
        INSTALLATION
        ~~~~~~~~~~~~
        
        ``pip install NanoPlot``
        
        | Upgrade to a newer version using:
        | ``pip install NanoPlot --upgrade``
        
        or
        
        | |conda badge|
        | ``conda install -c bioconda nanoplot``
        
        The script is written for python3.
        
        OUTPUT
        ~~~~~~
        
        NanoPlot creates: - a statistical summary - a number of plots - a html
        summary file
        
        USAGE
        ~~~~~
        
        ::
        
            NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw]
                            [-o OUTDIR] [-p PREFIX] [--maxlength N] [--minlength N]
                            [--drop_outliers] [--downsample N] [--loglength]
                            [--percentqual] [--alength] [--minqual N]
                            [--readtype {1D,2D,1D2}] [--barcoded] [-c COLOR]
                            [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                            [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]]
                            [--listcolors] [--no-N50] [--N50] [--title TITLE]
                            (--fastq file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --cram file [file ...] | --pickle pickle)
        
        
            General options:
              -h, --help            show the help and exit
              -v, --version         Print version and exit.
              -t, --threads THREADS Set the allowed number of threads to be used by the script
              --verbose             Write log messages also to terminal.
              --store               Store the extracted data in a pickle file for future plotting.
              --raw                 Store the extracted data in tab separated file.
              -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.
        
            Options for filtering or transforming input prior to plotting:
              --maxlength N         Drop reads longer than length specified.
              --minlength N         Drop reads shorter than length specified.
              --drop_outliers       Drop outlier reads with extreme long length.
              --downsample N        Reduce dataset to N reads by random sampling.
              --loglength           Logarithmic scaling of lengths in plots.
              --percentqual         Use qualities as theoretical percent identities.
              --alength             Use aligned read lengths rather than sequenced length (bam mode)
              --minqual N           Drop reads with an average quality lower than specified.
              --readtype            Which read type to extract information about from a summary file.
                                    One of 1D (default), 2D, 1D2
              --barcoded            Use if you want to split the summary file by barcode
        
            Options for customizing the plots created:
              -c, --color COLOR     Specify a color for the plots, must be a valid matplotlib color
              -f, --format          Specify the output format of the plots.
                                    One of png [default], eps,jpeg,jpg,pdf,pgf,ps,raw,rgba,svg,svgz,tif,tiff
              --plots               Specify which bivariate plots have to be made.
                                    One or more of kde (default), hex (default), dot (default), pauvre
              --listcolors          List the colors which are available for plotting and exit.
              --no-N50              Hide the N50 mark in the read length histogram
              --N50                 Show the N50 mark in the read length histogram
              --title TITLE         Add a title to all plots, requires quoting if using spaces
        
            Input data sources, one of these is required.:
              --fastq file [file ...]
                                    Data is in one or more default fastq file(s).
              --fastq_rich file [file ...]
                                    Data is in one or more fastq file(s) generated by albacore or MinKNOW with
                                    additional information concerning channel and time.
              --fastq_minimal file [file ...]
                                    Data is in one or more fastq file(s) generated by albacore or MinKNOW with
                                    additional information concerning channel and time. Minimal data is extracted
                                    swiftly without elaborate checks.
              --summary file [file ...]
                                    Data is in one or more summary file(s) generated by albacore.
              --bam file [file ...]
                                    Data is in one or more sorted bam file(s).
              --cram file [file ...]
                                    Data is in one or more sorted cram file(s).
              --pickle pickle       Data is a pickle file stored earlier.
        
        EXAMPLE USAGE
        ~~~~~~~~~~~~~
        
        .. code:: bash
        
            Nanoplot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed  
            NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot
            NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled
        
        This script now also provides read length vs mean quality plots in the
        '`pauvre <https://github.com/conchoecia/pauvre>`__'-style from
        [@conchoecia](https://github.com/conchoecia).
        
        `ACKNOWLEDGMENTS <https://github.com/wdecoster/NanoPlot/blob/master/ACKNOWLEDGMENTS.MD>`__
        ------------------------------------------------------------------------------------------
        
        I welcome all suggestions, bug reports, feature requests and
        contributions. Please leave an
        `issue <https://github.com/wdecoster/NanoPlot/issues>`__ or open a pull
        request. I will usually respond within a day, or rarely within a few
        days.
        
        PLOTS GENERATED
        ---------------
        
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Plot  | Fastq | Fastq | Fastq | Bam   | Summa | Optio | Style |
        |       |       | \_ric | \_min |       | ry    | ns    |       |
        |       |       | h     | imal  |       |       |       |       |
        +=======+=======+=======+=======+=======+=======+=======+=======+
        | Histo | x     | x     | x     | x     | x     | N50   |       |
        | gram  |       |       |       |       |       |       |       |
        | of    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Histo | x     | x     | x     | x     | x     | N50   |       |
        | gram  |       |       |       |       |       |       |       |
        | of    |       |       |       |       |       |       |       |
        | (log  |       |       |       |       |       |       |       |
        | trans |       |       |       |       |       |       |       |
        | forme |       |       |       |       |       |       |       |
        | d)    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar | x     | x     |       | x     | x     | log   | dot,  |
        | iate  |       |       |       |       |       | trans | hex,  |
        | plot  |       |       |       |       |       | forma | kde,  |
        | of    |       |       |       |       |       | tion  | pauvr |
        | lengt |       |       |       |       |       |       | e     |
        | h     |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | base  |       |       |       |       |       |       |       |
        | call  |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Heatm |       | x     |       |       | x     |       |       |
        | ap    |       |       |       |       |       |       |       |
        | of    |       |       |       |       |       |       |       |
        | reads |       |       |       |       |       |       |       |
        | per   |       |       |       |       |       |       |       |
        | chann |       |       |       |       |       |       |       |
        | el    |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Cumul |       | x     | x     |       | x     |       |       |
        | ative |       |       |       |       |       |       |       |
        | yield |       |       |       |       |       |       |       |
        | plot  |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Violi |       | x     | x     |       | x     |       |       |
        | n     |       |       |       |       |       |       |       |
        | plot  |       |       |       |       |       |       |       |
        | of    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        | over  |       |       |       |       |       |       |       |
        | time  |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Violi |       | x     |       |       | x     |       |       |
        | n     |       |       |       |       |       |       |       |
        | plot  |       |       |       |       |       |       |       |
        | of    |       |       |       |       |       |       |       |
        | base  |       |       |       |       |       |       |       |
        | call  |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        | over  |       |       |       |       |       |       |       |
        | time  |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar |       |       |       | x     |       |       | dot,  |
        | iate  |       |       |       |       |       |       | hex,  |
        | plot  |       |       |       |       |       |       | kde   |
        | of    |       |       |       |       |       |       |       |
        | align |       |       |       |       |       |       |       |
        | ed    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | seque |       |       |       |       |       |       |       |
        | nced  |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar |       |       |       | x     |       | log   | dot,  |
        | iate  |       |       |       |       |       | trans | hex,  |
        | plot  |       |       |       |       |       | forma | kde   |
        | of    |       |       |       |       |       | tion  |       |
        | perce |       |       |       |       |       |       |       |
        | nt    |       |       |       |       |       |       |       |
        | refer |       |       |       |       |       |       |       |
        | ence  |       |       |       |       |       |       |       |
        | ident |       |       |       |       |       |       |       |
        | ity   |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar |       |       |       | x     |       |       | dot,  |
        | iate  |       |       |       |       |       |       | hex,  |
        | plot  |       |       |       |       |       |       | kde   |
        | of    |       |       |       |       |       |       |       |
        | perce |       |       |       |       |       |       |       |
        | nt    |       |       |       |       |       |       |       |
        | refer |       |       |       |       |       |       |       |
        | ence  |       |       |       |       |       |       |       |
        | ident |       |       |       |       |       |       |       |
        | ity   |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | base  |       |       |       |       |       |       |       |
        | call  |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar |       |       |       | x     |       | log   | dot,  |
        | iate  |       |       |       |       |       | trans | hex,  |
        | plot  |       |       |       |       |       | forma | kde   |
        | of    |       |       |       |       |       | tion  |       |
        | mappi |       |       |       |       |       |       |       |
        | ng    |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | read  |       |       |       |       |       |       |       |
        | lengt |       |       |       |       |       |       |       |
        | h     |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        | Bivar |       |       |       | x     |       |       | dot,  |
        | iate  |       |       |       |       |       |       | hex,  |
        | plot  |       |       |       |       |       |       | kde   |
        | of    |       |       |       |       |       |       |       |
        | mappi |       |       |       |       |       |       |       |
        | ng    |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        | again |       |       |       |       |       |       |       |
        | st    |       |       |       |       |       |       |       |
        | basec |       |       |       |       |       |       |       |
        | all   |       |       |       |       |       |       |       |
        | quali |       |       |       |       |       |       |       |
        | ty    |       |       |       |       |       |       |       |
        +-------+-------+-------+-------+-------+-------+-------+-------+
        
        COMPANION SCRIPTS
        -----------------
        
        -  `NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing
           multiple runs
        -  `NanoStat <https://github.com/wdecoster/nanostat>`__: statistic
           summary report of reads or alignments
        -  `NanoFilt <https://github.com/wdecoster/nanofilt>`__: filtering and
           trimming of reads
        -  `NanoLyse <https://github.com/wdecoster/nanolyse>`__: removing
           contaminant reads (e.g. lambda control DNA) from fastq
        
        .. |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
        .. |conda badge| image:: https://anaconda.org/bioconda/nanoplot/badges/installer/conda.svg
           :target: https://anaconda.org/bioconda/nanoplot
        .. |Build Status| image:: https://travis-ci.org/wdecoster/NanoPlot.svg?branch=master
           :target: https://travis-ci.org/wdecoster/NanoPlot
        .. |Code Health| image:: https://landscape.io/github/wdecoster/NanoPlot/master/landscape.svg?style=flat
           :target: https://landscape.io/github/wdecoster/NanoPlot/master
        
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
Requires-Python: >=3
