Metadata-Version: 1.2
Name: NanoComp
Version: 0.12.2
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] [-o OUTDIR] [-p PREFIX] [--verbose]
                            [--readtype {1D,2D,1D2}] [--split_runs TSV_FILE]
                            [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                            [-n names [names ...]] [--plot {violin,box}]
                            (--fastq files [files ...] | --summary files [files ...] | --bam files [files ...])
        
        
            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
              -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.
              --verbose             Write log messages also to terminal.
        
              Options for customizing the plots created:
                -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)
        
              Input data sources, one of these is required.:
                --fastq files [files ...]
                                      Data is in default fastq format.
                --summary files [files ...]
                                      Data is a summary file generated by albacore.
                --bam files [files ...]
                                      Data as a sorted bam file.
        
            Options for filtering or transforming input prior to plotting:
              --readtype            Which read type to extract information about from summary. Options are 1D, 2D, 1D2
              --split_runs TSV_FILE File: Split the summary on run IDs and use names in tsv file.
                                    Mandatory header fields are 'NAME' and 'RUN_ID'.
        
        `Example file for
        --split\_runs <https://github.com/wdecoster/nanocomp/blob/master/extra/split_file.tsv>`__
        
        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
Requires-Python: >=3
