error in matching contigs to barcodes

[kostasandriotis07]

Hello,

I have an issue with running barcoding of my contigs in Phyluce. I read and followed the instructions provided to Julia a couple of months ago as she reported having the same issue. Under phyluce/bin/[phyluce_assembly_match_contigs_to_barcodes - and on line 136-139 I replaced what was there before with the following code:

r = requests.get(
"http://v4.boldsystems.org/index.php/Ids_xml",
params=payload,
)

After running my code again, Phyluce failed again. Could you please help me with this? Is there any other way I can fix this problem?

Thank you for your help!

Kostas

[brantfaircloth]

This looks to be related to #369. I think that something is sometimes encoded weirdly in the XML that is returned from BOLD. There seem to be a couple of work-arounds... One that I've tried (that seems to work so far) is to edit lines ~140 to remove:

root = ElementTree.fromstring(r.content)

and replace that with:

parser = ElementTree.XMLParser(encoding="utf-8")
root = ElementTree.fromstring(r.content, parser=parser)