Metadata-Version: 1.1
Name: ucsc_snapshots
Version: 0.1.6
Summary: fetch images from the UCSC genome browser using BED regions
Home-page: https://github.com/jayhesselberth/ucsc_snapshots
Author: Jay Hesselberth
Author-email: jay.hesselberth@gmail.com
License: MIT
Description: # ucsc\_snapshots documentation
        
        **Version**: 0.1.6
        
        ## 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-<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
        
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
