hubward 0.2.2

Manage the visualization of large amounts of other people's [often messy] genomics data

hubward

A common question when reading an interesting paper is, “how does relate to my favorite gene locus?”. To address this question, usually we need to download the supplemental data, figure out what format it’s in, convert it to some other useful format, and visualize it alongside our own data.

hubward helps manage this process, lowering the effort required to track, manage, organize, and upload many studies for cross-comparison in the UCSC Genome Browser.

Data are organized into track hubs on the UCSC Genome Browser, and the name hubward indicates the direction in which data are moved into these track hubs. It can also refer to a direction in other complex systems.

The separate repository, hubward-studies, contains examples of prepared track hubs. Subsets of these can be combined into user-defined hubs, or can serve as examples for preparing other studies.

Documentation can be found at https://daler.github.io/hubward.

Overview

This poster gives an overview of hubward, and provides a worked example.

Further details can be found in the full documentation.

History

0.2.2 (2016-01-20)

• Support for liftover of BAMs (includes a workaround for Crossmap bug that segfaulted on liftovers with a specified output filename in the test environment).

• When lifting over between assemblies and the source assembly doesn’t match what is configured for a track, raise a ValueError.

• For lifted-over studies, the metadata.yaml config keeps track of the liftover history in the new study/liftover section

• improved test environment setup

• improved tests (checking for existence of uploaded files)

0.2.1 (2015-12-05)

• if the description field is empty or missing, fill in the contents of README as documentation.

• add functools32 to requirements.txt (thanks Titus Brown)

• fixes to hubward liftover:

  • downloaded chainfiles are cached

  • skip tracks where assembly of track differs from the requested –from_assembly

  • upon lifting over, add a note to the description of the study’s metadata.yaml to reflect this and also as a comment in the YAML file.

  • workaround for a bug in CrossMap on BED9+ files. The thickStart and thickEnd fields were not being lifted over correctly.

• use pycurl for downloading for better handling of URL redirects. This happens, for example, when downloading supplemental data from ScienceDirect

• less verbose bigbed/bigwig conversion

• allow optional fields in metadata to be blank

• improvements to testing framework

0.2.0 (2015-10-24)

Streamlining of the code and CLI. This causes some backward incompatibility with metadata.yaml config files in version 0.1.0, in particular, the “source” section is now required. There is now a defined schema for the metadata and the grouping files so that future changes can be validated and automatically fixed.

0.1.0 (2014-01-11)

• First release on PyPI.