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توضیحات

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

ویژگی	مقدار
سیستم عامل	-
نام فایل	dnacol-0.4
نام	dnacol
نسخه کتابخانه	0.4
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Nils Koelling
ایمیل نویسنده	git@nk.gl
آدرس صفحه اصلی	https://github.com/koelling/dnacol/
آدرس اینترنتی	https://pypi.org/project/dnacol/
مجوز	MIT

``dnacol`` and ``pcol`` ======================== Color DNA/RNA bases, protein amino acid codes and quality scores in terminal output About ----- This is a python script to color DNA, RNA and protein sequences in the terminal. If called using ``dnacol``, 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. If called using ``pcol``, it will instead color protein sequences encoded as amino acid one-letter codes. Screenshots ~~~~~~~~~~~ .. image:: https://raw.githubusercontent.com/koelling/dnacol/master/screenshots_v0.4.png Format-specific coloring ~~~~~~~~~~~~~~~~~~~~~~~~ By default, ``dnacol`` will find and color all strings of one or more DNA/RNA letters and ``pcol`` will color all strings of the twenty standard amino acid letters. However, they 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`` and ``pcol`` 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 Colormaps ~~~~~~~~~ The script support different colormaps, which specify a color for each possible letter of the sequence. These are shown in ``dnacol --help``. When called using ``dnacol``, the script will use the ``dna_brgy`` colormap by default, while ``pcol`` will use the ``protein`` colormap. You can change the ``dnacol`` colormap using a configuration file (see below). Options ------- :: -w, --wide wide output (add spaces around each base) -f FORMAT, --format FORMAT file format (auto|text|sam|vcf|fastq|fasta) Configuration ------------- You can create a configuration file in YAML format called ``/etc/dnacol`` or ``~/.dnacol`` to change the behavior of this script. At the moment, the only setting available is the colormap to use for DNA sequences. See see ``dnacol --help`` for examples of the colormaps that are available. To use the ``gbyr`` instead of the ``brgy`` colormap, set the ``dna_colormap`` option like this: :: dna_colormap: gbyr Download/Install ---------------- To install, use ``pip``:: pip install dnacol If the system-wide directory is not writable, you can install to your home directory with:: pip install dnacol --user Alternatively, you can clone this git repository and use the provided ``setup.py`` script. :: git clone https://github.com/koelling/dnacol.git cd dnacol && python setup.py install ``dnacol`` has been tested with Python 2.7 and Python 3.5 and 3.6. Examples -------- :: #read gzipped file dnacol examples/phix.fa.gz | head #pipe from stdin head examples/reads.txt | dnacol --wide #use `pcol` for protein sequences pcol examples/hras.fa #use `less -R` to display colors in less dnacol examples/phix.fa.gz | less -R

نحوه نصب

نصب پکیج whl dnacol-0.4:

pip install dnacol-0.4.whl

نصب پکیج tar.gz dnacol-0.4:

pip install dnacol-0.4.tar.gz