Entering edit mode
3.9 years ago
Axel.Kowald
•
0
Hello Everybody,
I installed Biopython 1.77 and want to read a record from the NCBI Homologene db like this:
handle = Bio.Entrez.efetch(db='HomoloGene', id=134538, retMode='xml')
recordH = Bio.Entrez.read(handle)
Unfortunately read(handle) produces an error like:
"ValueError: As the XML data contained neither a Document Type Definition (DTD) nor an XML Schema for tag 'Entrez-Homologene-Set', Bio.Entrez is unable to parse these data. We recommend using a generic XML parser from the Python standard library instead, for example ElementTree."
Any idea what I'm doing wrong ?
Many thanks
I don't think you are doing anything wrong. Looks like biopython is not able to parse
xml
format that is returned.If you don't specify
xml
format you will get the following. Perhaps you can parse that instead.Okay, thanks. I will then parse the text format.