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fetch images from the UCSC genome browser using BED regions

Project description

# 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:



## 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-<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

pip install ucsc_snapshots

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