Tile generation for big data

Project description

Clodius

Displaying large amounts of data often requires first turning it into not-so-large amounts of data. Clodius is a program and library designed to aggregate large datasets to make them easy to display at different resolutions.

Demo

Install the clodius package:

pip install clodius

And use it aggregate a bigWig file:

curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
  > /tmp/sample.short.bed
clodius aggregate bedfile /tmp/sample.short.bed

The output files can then be displayed using higlass-manage. For more information about viewing these types of files take a look at the higlass docs.

More examples are available.

File Types

Non-genomic Rasters
- TSV Files
Genomic Data

Development

The recommended way to develop clodius is to use a conda environment and install clodius with develop mode:

pip install -e .

Testing

The unit tests for clodius can be run using pytest:

pytest

Individual unit tests can be specified by indicating the file and function they are defined in:

pytest test/cli_test.py:test_clodius_aggregate_bedgraph

Project details

Release history Release notifications | RSS feed

0.20.1

May 15, 2023

0.20.0

Mar 9, 2023

This version

0.19.0

May 31, 2022

0.18.1

Mar 20, 2022

0.18.0

Dec 22, 2021

0.17.1

Nov 19, 2021

0.17.0

Aug 10, 2021

0.16.0

Apr 12, 2021

0.15.4

Nov 13, 2020

0.15.3

Oct 25, 2020

0.15.2

Oct 11, 2020

0.15.1

Aug 26, 2020

0.15.0

Aug 9, 2020

0.14.3

Mar 5, 2020

0.14.2

Feb 7, 2020

0.14.1

Jan 28, 2020

0.14.0

Jan 16, 2020

0.13.1

Dec 3, 2019

0.13.0

Dec 1, 2019

0.12.0

Nov 13, 2019

0.11.4

Oct 17, 2019

0.11.3

Oct 6, 2019

0.11.2

Sep 28, 2019

0.11.1

Sep 28, 2019

0.11.0

Sep 23, 2019

0.10.13

Jul 7, 2019

0.10.12

Jul 7, 2019

0.10.11

Jul 6, 2019

0.10.10

Jul 4, 2019

0.10.9

Jul 4, 2019

0.10.8

May 9, 2019

0.10.7

May 7, 2019

0.10.6

Mar 7, 2019

0.10.4

Feb 20, 2019

0.10.3

Feb 11, 2019

0.10.2

Feb 6, 2019

0.10.1

Jan 24, 2019

0.10.0

Jan 19, 2019

0.10.0rc4 pre-release

Dec 10, 2018

0.10.0rc3 pre-release

Dec 5, 2018

0.10.0rc2 pre-release

Nov 24, 2018

0.10.0rc1 pre-release

Nov 23, 2018

0.9.4

Sep 27, 2018

0.9.3

Jun 27, 2018

0.9.2

Jun 21, 2018

0.9.1

May 7, 2018

0.9.0

May 7, 2018

0.8.0

May 7, 2018

0.7.4

Feb 16, 2018

0.7.3

Jan 31, 2018

0.7.2

Dec 4, 2017

0.7.1

Dec 4, 2017

0.7.0

Oct 4, 2017

0.6.5

Jul 14, 2017

0.6.4

Jul 13, 2017

0.6.3

Jul 13, 2017

0.6.2

Jul 13, 2017

0.6.1

Jul 11, 2017

0.6.0

Jul 11, 2017

0.5.0

Apr 17, 2017

0.4.5

Mar 29, 2017

0.4.4

Mar 29, 2017

0.4.3

Mar 29, 2017

0.4.2

Mar 21, 2017

0.4.1

Mar 21, 2017

0.4.0

Mar 21, 2017

0.3.4

Jan 18, 2017

0.3.3

Jan 18, 2017

0.3.2

Jan 17, 2017

0.3.1

Jan 13, 2017

0.3.0

Jan 5, 2017

0.2.18

Jan 13, 2017

0.2.17

Dec 15, 2016

0.2.16

Dec 8, 2016

0.2.15

Dec 7, 2016

0.2.14

Nov 25, 2016

0.2.13

Nov 25, 2016

0.2.12

Nov 25, 2016

0.2.10

Nov 25, 2016

0.2.9

Nov 25, 2016

0.2.8

Nov 25, 2016

0.2.7

Nov 25, 2016

0.2.6

Nov 25, 2016

0.2.5

Nov 25, 2016

0.2.3

Nov 25, 2016

0.2.2

Nov 25, 2016

0.2.1

Nov 25, 2016

0.2.0

Nov 25, 2016

0.1.2

Nov 11, 2016

0.1.1

Nov 10, 2016

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