ucsc_snapshots documentation

Version: 0.1.8

Summary

ucsc_snapshots retrieves pictures from UCSC Genome Browser based on coordinates specified from BED3+ file and a session ID (hgsid).

UCSC Genome Browser should be set up with tracks prior to using the utility and saved as a session. This includes all track settings, sizes etc. Once these are setup, you can load the page source and identify the hgsid by searching for "hgsid="

Supply the hgsid and a BED file. Images will be retrieved based on the coordinates in the BED file and saved to the directory as:

ucsc-snapshots-<hgsid>/chrom-start-end.pdf

ucsc-snapshots-<hgsid>/chrom-start-end.png

Warnings

if you have many regions, you may need to run this overnight as thet UCSC limit s 1 request per 15 sec and 5000 requests per day.

Beware of multiple procs accessessing the same hgsid at the same time, they will affect each other's strand settings

Examples

The simplest case, just fetch images:

ucsc_snapshots BED3+ SESSIONID

Retrieve snapshots maintaining the display with 5'->3' orientation using the strand field from the BED file:

ucsc_snapshots BED3+ SESSIONID --reverse-display

Add an annotation to the output directory (directory becomes ucsc-snapshots--annotation/):

ucsc_snapshots BED3+ SESSIONID --dir-annotation celltype=MCF7

Output PNG files only (default is PDF and PNG):

ucsc_snapshots BED3+ SESSIONID --img-types png

Installation

pip install ucsc_snapshots