Metadata-Version: 1.1
Name: dnacol
Version: 0.3.1
Summary: Display FASTA/FASTQ/SAM/VCF files with colored DNA/RNA bases and quality scores in the terminal
Home-page: https://github.com/koelling/dnacol/
Author: Nils Koelling
Author-email: git@nk.gl
License: MIT
Download-URL: https://github.com/koelling/dnacol/archive/v0.3.1.tar.gz
Description: dnacol
        ======
        
        Color DNA/RNA bases and quality scores in terminal output
        
        About
        -----
        
        This is a python script to color DNA or RNA sequences in the terminal.
        It will read lines from STDIN or from a file and color all strings of
        DNA/RNA it can find. In addition, it can also color phred-encoded
        quality scores in FASTQ/SAM files.
        
        Format-specific coloring
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        By default, ``dnacol`` will color all strings of ``[ACGTUN]+``. However,
        it will also recognize a few standard file formats and apply more
        targeting coloring. When reading a file, these formats will
        automatically be recognized based on their file extensions. When reading
        from STDIN, ``dnacol`` will try to identify the format based on the data
        itself (for FASTQ/SAM/VCF files). The format can also be specified using
        the ``--format`` option.
        
        -  SAM format (``--format=sam``, automatically enabled when filename
           ends in ``.sam`` or a line matching the SAM format is found)
        
           -  Ignore headers, color the SEQ column as DNA and the QUAL column as
              quality scores
        
        -  FASTQ format (``--format=fastq``, automatically enabled when filename
           ends in ``.fastq`` or ``.fq`` or the first four lines match the FASTQ
           format)
        
           -  Color the second line of every read as DNA
           -  Color the fourth line of every read as quality scores
        
        -  VCF format (``--format=vcf``, automatically enabled when filename
           ends in ``.vcf`` or a VCF header line is found)
        
           -  Ignore comments, only color the REF and ALT column
        
        -  FASTA format (``--format=fasta``, automatically enabled when filename
           ends in ``.fasta`` or ``.fa``)
        
           -  Ignore sequence identifiers
        
        Options
        -------
        
        ::
        
            -w, --wide
                wide output (add spaces around each base)
            -f FORMAT, --format FORMAT
                file format (auto|text|sam|vcf|fastq|fasta)
        
        Download/Install
        ----------------
        
        Tested with Python 2.7 and Python 3.6. To install, clone this git
        repository and use the provided ``setup.py`` script. When installed
        correctly, ``dnacol`` will simply be available as ``dnacol`` in the
        command line.
        
        ::
        
            #download
            git clone https://github.com/koelling/dnacol.git
        
            #install
            cd dnacol && python setup.py install    
        
            #or: install to home directory (if system-wide directory is not writable)
            cd dnacol && python setup.py install --user
        
        Examples
        --------
        
        ::
        
            #read gzipped file
            dnacol examples/phix.fa.gz | head
        
            #pipe from stdin
            head examples/reads.txt | dnacol --wide
        
            #use `less -R` to display colors in less
            dnacol examples/phix.fa.gz | less -R
        
        Screenshots
        -----------
        
        .. image:: screenshots_v0.3.png
        
Keywords: dnacol rnacol rna dna quality phred color colour bases console terminal stdout
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
