.. Squiggle documentation master file, created by sphinx-quickstart on Thu Jul 5 23:24:54 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Squiggle ======== |DOI| |Build Status| |Docs| |PyPI| `Squiggle `_ is a two-dimensional DNA sequence visualization library that can turn FASTA sequence files like this: .. code-block:: text >lcl|NC_000011.10_cds_NP_000509.1_1 [gene=HBB] ATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAG TTGGTGGTGAGGCCCTGGGCAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGG GGATCTGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGT GCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACT GTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCA TCACTTTGGCAAAGAATTCACCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAAT GCCCTGGCCCACAAGTATCACTAA >lcl|NC_005100.4_cds_NP_150237.1_1 [gene=HBB] ATGGTGCACCTGACTGATGCTGAGAAGGCTGCTGTTAATGGCCTGTGGGGAAAGGTGAACCCTGATGATG TTGGTGGCGAGGCCCTGGGCAGGCTGCTGGTTGTCTACCCTTGGACCCAGAGGTACTTTGATAGCTTTGG GGACCTGTCCTCTGCCTCTGCTATCATGGGTAACCCTAAGGTGAAGGCCCATGGCAAGAAGGTGATAAAC GCCTTCAATGATGGCCTGAAACACTTGGACAACCTCAAGGGCACCTTTGCTCATCTGAGTGAACTCCACT GTGACAAGCTGCATGTGGATCCTGAGAACTTCAGGCTCCTGGGCAACATGATTGTGATTGTGTTGGGCCA CCACCTGGGCAAGGAATTCTCCCCCTGTGCACAGGCTGCCTTCCAGAAGGTGGTGGCTGGAGTGGCCAGT GCCCTGGCTCACAAGTACCACTAA into gorgeous, interactive visualizations like this: .. raw:: html :file: figures/hbb_comparison.html Installation ------------ If you don't have Python 3.4 or greater installed, be sure to `get it `_. To get the current stable version of Squiggle, run:: $ pip install squiggle Or, alternatively, if you want to get the latest development version:: $ pip install git+https://github.com/Lab41/squiggle.git Usage ----- Using Squiggle is as easy as:: $ squiggle your_sequence.fasta Squiggle has tons of options available to make beautiful, interactive visualizations of DNA sequences. To get a full rundown of the various option, take a look at the :ref:`guide`. Citation -------- Using Squiggle in your research? Please cite it! - Lee, B. D. (2018). Squiggle: a user-friendly two-dimensional DNA sequence visualization tool. *Bioinformatics*. `doi:10.1093/bioinformatics/bty807 `_ .. code-block:: bibtex @article{Lee2018, doi = {10.1093/bioinformatics/bty807}, url = {https://doi.org/10.1093/bioinformatics/bty807}, year = {2018}, month = {sep}, publisher = {Oxford University Press ({OUP})}, author = {Benjamin D Lee}, editor = {John Hancock}, title = {Squiggle: a user-friendly two-dimensional {DNA} sequence visualization tool}, journal = {Bioinformatics} } Table of Contents ----------------- .. toctree:: :maxdepth: 2 methods user_guide api cli license Indices and tables ------------------ * :ref:`genindex` * :ref:`modindex` * :ref:`search` .. |DOI| image:: https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbty807-brightgreen.svg :target: https://doi.org/10.1093/bioinformatics/bty807 .. |Build Status| image:: https://travis-ci.org/Lab41/squiggle.svg?branch=master :target: https://travis-ci.org/Lab41/squiggle .. |Docs| image:: http://readthedocs.org/projects/squiggle/badge/?version=latest :target: http://squiggle.readthedocs.io/en/latest/?badge=latest .. |PyPI| image:: https://img.shields.io/pypi/v/squiggle.svg :target: https://pypi.org/project/squiggle/