fetch images from the UCSC genome browser using BED regions
Project description
# ucsc_snapshots documentation
Version: 0.1.5
## 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 (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)
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: currently requires the github development version.
path.py
pybedtools
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