GenBank parser KeyError: 'IdList' (hard to reproduce)
Created by: mutalyzerbot
Original ticket: https://humgenprojects.lumc.nl/trac/mutalyzer/ticket/51 Original date: 2011/04/12 Original reporter: m DOT vermaat DOT hg AND lumc DOT nl
A variant on a DMD slice (e.g. UD_129433404385(DMD_v001):c.163-4_240+6del) gives random errors that are hard to reproduce.
The problem is in the GenBank parser (__transcriptToProtein):
handle # Entrez.esearch(db"nucleotide", term = transcriptAcc)
result = Entrez.read(handle)
handle.close()
transcriptGI = result["IdList"][0]
It seems that sometimes Entrez.esearch is called with term='NR_031646'
, which results in a result
that has no IdList
attribute.
It is not clear to me when this happens. Most of the time everything is fine, so there seems to be some nondeterminism here...