iqtlabs / squiggle

📈 DNA Sequence Visualization for Humans

This repository has moved to https://github.com/Benjamin-Lee/squiggle

Squiggle is a two-dimensional DNA sequence visualization library that can turn FASTA sequence files like this:

>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:

(Click the picture to view an interactive version.)

Installation

If you don't have Python 3.5 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 look at the documentation here.

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

@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}
}

squiggle's Issues

Add type annotations

HTML preview in README is broken

Use balanced curves for nucleotides

Wouldn't it be better to use curves (i.e., shapes) of equal areas for each of the nucleotides? Right now, A and C have areas of + and - 0.25 units respectively, while G and T have areas of + and - 0.5 units respectively.

In some applications, like data storage in DNA, it is likely that optimal encodings have an equal number of each of the nucleotides, and having balanced representations could make it easier to spot imbalances and thereby compare different encodings visually.

This won't eliminate any of the other benefits stated in the blog post, but I think it will broaden the application of this visualization.

Update index.rst in docs/

This requires:

• Update badges
• Update Python version dependency

error in examples

Hi,
I have installed squiggle by pip3 but I got this error in running examples:
squiggle ecol.heg.fasta

Visualizing each sequence in black.
0%| | 0/274 [00:00<?, ? seqs/s]BokehDeprecationWarning: 'legend' keyword is deprecated, use explicit 'legend_label', 'legend_field', or 'legend_group' keywords instead
Traceback (most recent call last):
File "/usr/local/bin/squiggle", line 11, in
load_entry_point('squiggle==0.3.1', 'console_scripts', 'squiggle')()
File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.6/dist-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/squiggle/cli.py", line 223, in visualize
color=seq.color)
File "/usr/local/lib/python3.6/dist-packages/bokeh/plotting/_decorators.py", line 54, in wrapped
return create_renderer(glyphclass, self, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/bokeh/plotting/_renderer.py", line 126, in create_renderer
update_legend(plot, legend_kwarg, glyph_renderer)
File "/usr/local/lib/python3.6/dist-packages/bokeh/plotting/_legends.py", line 56, in update_legend
_LEGEND_KWARG_HANDLERS[kwarg](value, legend, glyph_renderer)
File "/usr/local/lib/python3.6/dist-packages/bokeh/plotting/_legends.py", line 82, in _handle_legend_deprecated
raise ValueError("Bad 'legend' parameter value: %s" % label)
ValueError: Bad 'legend' parameter value: None

The only fasta that I can successfully run is

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

Drop dependency on box

We should just be able to use a named tuple instead.

Update logo

For simplicity, we'll use the DNAvisualization.org logo

Update badge on README