[Biopython] About BLAST parser
Manu Tamminen
mavata at gmail.com
Thu Oct 22 09:45:13 UTC 2009
I have a problem with the Biopython BLAST parser. I'm using the parser
to extract relevant information from an XML result file into a tab-
separated table. It seems the XML file occasionally contains errors
that cause the script to abort. This is especially common and annoying
with sequence alignments that contain thousands of sequences.
Is it possible to write the script so that when an error occurs, the
script would jump into the next sequence rather than abort completely?
I will include below an example of such error. This error is about a
mismatched tag - sometimes the error has also been about a missing tag.
for blast_record in blast_records:
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/Blast/NCBIXML.py", line 660, in parse
expat_parser.Parse(text, True) # End of XML record
xml.parsers.expat.ExpatError: mismatched tag: line 82921, column 4
Any help appreciated! Thanks!
Manu
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