ucsc_snapshots 0.1.4

fetch images from the UCSC genome browser using BED regions

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ucsc_snapshots documentation
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: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``