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  • r.rosati
    Member
    • Aug 2015
    • 95

    Opening a dbSNP page from IGV?

    Hello,
    I often want to search dbSNP entries I find while browsing exomes in IGV. Apparently left-clicking the dbSNP track entry doesn't have this functionality (as opposed to, say, the RefSeq Genes track).
    At the moment, to avoid re-writing the rs I'm just using a small Python 3 script - it's trivial but if anybody else wants it, it's this one:

    Code:
    #!/usr/bin/env python3
    '''
    Opens Google and dbSNP webpages to a rs SNP copied from IGV.
    Usage: right-click the rs on IGV, select "Copy details to clipboard",
    then execute the script.
    '''
    
    from tkinter import Tk, messagebox
    import re
    import webbrowser
    
    a = Tk().clipboard_get()
    rs = re.search('<b>rs(\d*?)</b>', a)
    if rs:
        webbrowser.open('http://www.google.com.br/search?q=rs'
                        '{0}'.format(rs.group(1)))
        webbrowser.open('http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs='
                        '{0}'.format(rs.group(1)))
    else:
        messagebox.showwarning('Warning', 'No rs found in clipboard.')
    It captures the clipboard, so I use it by right-clicking the SNP in IGV, selecting "Copy details to clipboard", and then executing the script right away. (...It beats retyping the SNP.)

    But I was wondering if there's anything I'm missing on IGV? I found it strange that this functionality isn't available, so maybe it is and I'm not finding it.
    Thanks!
    Last edited by r.rosati; 05-18-2016, 12:29 PM. Reason: Added description & shebang

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