{ "info": { "author": "Nils Koelling", "author_email": "git@nk.gl", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: MIT License", "Operating System :: MacOS", "Operating System :: Unix", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3" ], "description": "``dnacol`` and ``pcol``\n========================\n\nColor DNA/RNA bases, protein amino acid codes and quality scores in terminal output\n\nAbout\n-----\n\nThis is a python script to color DNA, RNA and protein sequences in the terminal.\nIf called using ``dnacol``, it will read lines from STDIN or from a file and color all strings of\nDNA/RNA it can find. In addition, it can also color phred-encoded\nquality scores in FASTQ/SAM files.\nIf called using ``pcol``, it will instead color protein sequences encoded as amino acid one-letter codes.\n\nScreenshots\n~~~~~~~~~~~\n\n.. image:: https://raw.githubusercontent.com/koelling/dnacol/master/screenshots_v0.4.png\n\nFormat-specific coloring\n~~~~~~~~~~~~~~~~~~~~~~~~\n\nBy default, ``dnacol`` will find and color all strings of one or more DNA/RNA letters and\n``pcol`` will color all strings of the twenty standard amino acid letters.\nHowever, they will also recognize a few standard file formats and apply more\ntargeting coloring. When reading a file, these formats will\nautomatically be recognized based on their file extensions. When reading\nfrom STDIN, ``dnacol`` and ``pcol`` will try to identify the format based on the data\nitself (for FASTQ/SAM/VCF files). The format can also be specified using\nthe ``--format`` option.\n\n- SAM format (``--format=sam``, automatically enabled when filename\n ends in ``.sam`` or a line matching the SAM format is found)\n\n - Ignore headers, color the SEQ column as DNA and the QUAL column as\n quality scores\n\n- FASTQ format (``--format=fastq``, automatically enabled when filename\n ends in ``.fastq`` or ``.fq`` or the first four lines match the FASTQ\n format)\n\n - Color the second line of every read as DNA\n - Color the fourth line of every read as quality scores\n\n- VCF format (``--format=vcf``, automatically enabled when filename\n ends in ``.vcf`` or a VCF header line is found)\n\n - Ignore comments, only color the REF and ALT column\n\n- FASTA format (``--format=fasta``, automatically enabled when filename\n ends in ``.fasta`` or ``.fa``)\n\n - Ignore sequence identifiers\n\n\nColormaps\n~~~~~~~~~\nThe script support different colormaps, which specify a color for each possible letter of the sequence.\nThese are shown in ``dnacol --help``. When called using ``dnacol``, the script will use the ``dna_brgy`` colormap by default,\nwhile ``pcol`` will use the ``protein`` colormap. You can change the ``dnacol`` colormap using a configuration file (see below).\n\nOptions\n-------\n\n::\n\n -w, --wide\n wide output (add spaces around each base)\n -f FORMAT, --format FORMAT\n file format (auto|text|sam|vcf|fastq|fasta)\n\nConfiguration\n-------------\nYou can create a configuration file in YAML format called ``/etc/dnacol`` or ``~/.dnacol`` to change the behavior of this script.\nAt the moment, the only setting available is the colormap to use for DNA sequences.\nSee see ``dnacol --help`` for examples of the colormaps that are available.\n\nTo use the ``gbyr`` instead of the ``brgy`` colormap, set the ``dna_colormap`` option like this:\n\n::\n \n dna_colormap: gbyr\n\nDownload/Install\n----------------\n\nTo install, use ``pip``::\n\n pip install dnacol\n\nIf the system-wide directory is not writable, you can install to your home directory with::\n\n pip install dnacol --user\n\nAlternatively, you can clone this git\nrepository and use the provided ``setup.py`` script.\n\n::\n\n git clone https://github.com/koelling/dnacol.git\n cd dnacol && python setup.py install\n\n``dnacol`` has been tested with Python 2.7 and Python 3.5 and 3.6.\n\nExamples\n--------\n\n::\n\n #read gzipped file\n dnacol examples/phix.fa.gz | head\n\n #pipe from stdin\n head examples/reads.txt | dnacol --wide\n\n #use `pcol` for protein sequences\n pcol examples/hras.fa\n\n #use `less -R` to display colors in less\n dnacol examples/phix.fa.gz | less -R\n", "description_content_type": null, "docs_url": null, "download_url": "https://github.com/koelling/dnacol/archive/v0.4.tar.gz", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/koelling/dnacol/", "keywords": "dnacol rnacol pcol rna dna protein amino acid quality phred color colour bases console terminal stdout", "license": "MIT", "maintainer": "", "maintainer_email": "", "name": "dnacol", "package_url": "https://pypi.org/project/dnacol/", "platform": "any", "project_url": "https://pypi.org/project/dnacol/", "project_urls": { "Download": "https://github.com/koelling/dnacol/archive/v0.4.tar.gz", "Homepage": "https://github.com/koelling/dnacol/" }, "release_url": "https://pypi.org/project/dnacol/0.4/", "requires_dist": null, "requires_python": "", "summary": "Display FASTA/FASTQ/SAM/VCF files with colored DNA/RNA bases and quality scores (`dnacol`) or a protein sequence with colored amino acid codes (`pcol`) in the terminal", "version": "0.4" }, "last_serial": 3135046, "releases": { "0.3.1": [ { "comment_text": "", "digests": { "md5": "c85cd94a96eedbe3ea56349529e5c70b", "sha256": "ef9d5b85b6f59abf59d47b3f6a3aff4b9aee83a386473d2bfe42a997ee6f4a31" }, "downloads": -1, "filename": "dnacol-0.3.1.tar.gz", "has_sig": false, "md5_digest": "c85cd94a96eedbe3ea56349529e5c70b", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 6414, "upload_time": "2017-08-01T13:07:01", "url": "https://files.pythonhosted.org/packages/fe/4e/69b6deec09ba3158b6bb64ab33e517c3bdcdf6fdfd476cf2104e4cdbd020/dnacol-0.3.1.tar.gz" } ], "0.3.2": [ { "comment_text": "", "digests": { "md5": "f39c5c328f4d8df3cc96dac27a326688", "sha256": "d094d80d13c44c7ff6b5a8ca268ba5d18a6a042c709ef7ad8532742381b52d51" }, "downloads": -1, "filename": "dnacol-0.3.2.tar.gz", "has_sig": false, "md5_digest": "f39c5c328f4d8df3cc96dac27a326688", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 6492, "upload_time": "2017-08-01T13:34:19", "url": "https://files.pythonhosted.org/packages/80/77/91c570ef68486250ecf273608b8838b8c118b9dfa2c87d4d03edf798a1ed/dnacol-0.3.2.tar.gz" } ], "0.4": [ { "comment_text": "", "digests": { "md5": "2aecf1c35fef40ba9790e53974c361e0", "sha256": "3f9e4d22a28993ba40473f6698767a551ccc55479d8b74c85fe4b0247f181bc4" }, "downloads": -1, "filename": "dnacol-0.4.tar.gz", "has_sig": false, "md5_digest": "2aecf1c35fef40ba9790e53974c361e0", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8108, "upload_time": "2017-08-30T15:06:56", "url": "https://files.pythonhosted.org/packages/ee/39/cece018d186c50f9cf58df3467291b42c5858373371f813218670e03d728/dnacol-0.4.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "2aecf1c35fef40ba9790e53974c361e0", "sha256": "3f9e4d22a28993ba40473f6698767a551ccc55479d8b74c85fe4b0247f181bc4" }, "downloads": -1, "filename": "dnacol-0.4.tar.gz", "has_sig": false, "md5_digest": "2aecf1c35fef40ba9790e53974c361e0", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 8108, "upload_time": "2017-08-30T15:06:56", "url": "https://files.pythonhosted.org/packages/ee/39/cece018d186c50f9cf58df3467291b42c5858373371f813218670e03d728/dnacol-0.4.tar.gz" } ] }