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Old 05-18-2016, 11:52 AM   #1
Location: Brazil

Join Date: Aug 2015
Posts: 92
Default Opening a dbSNP page from IGV?

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:

#!/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 ='<b>rs(\d*?)</b>', a)
if rs:''
    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.

Last edited by r.rosati; 05-18-2016 at 12:29 PM. Reason: Added description & shebang
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