Skip to main content

fetch images from the UCSC genome browser using BED regions

Project description

********************************
ucsc_snapshots documentation
********************************

:Author: Jay Hesselberth <jay dot hesselberth at gmail dot com>
:Organization: University of Colorado School of Medicine
:Version: |version|

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
========

1. if you have many regions, you may need to run this overnight
(e.g. via a job submitted to the LSF night queue), otherwise UCSC could
throttle your connection (limit 1 request / 15 sec, 5000 requests per day)

1. 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-<hgsid>-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
============

The following requirements can be installed with ``pip``:

+ ``ucscsession``
+ ``path.py``
+ ``pybedtools``

Project details


Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page