Parsing <Iteration_query-def> <Hit_def> from BLAST xml file
I have results of command-line BLASTp and I would like to convert to table format. Seems BLASTp -outfmt 6 cannot parse <hit_def> field from xml file, right?
I'm thinking about Biopython. Thanks
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blastp -outfmt nis a way to define the output format. That program is not going to parse results from a previous run of blastp. What format did you actually use for the output?I know what is -outfmt genomax2. I'm using -outfmt 5 to get xml output and trying to get a table with <iteration_query-def> <hit_def>. Seems outfmt 6 can't get hit description.
Since you had outfmt 6 in your original post I was not sure.
So you already have some code you are using? If not, take a look at the examples in the biopython tutorial here.
A practical example is in this thread: Extracting Accession Numbers With Ncbixml.Parse
Did you meant subject title for outfmt 6?
Yes. Thank you very much @genomax2. I just saw the request here http://blastedbio.blogspot.co.il/2012/05/blast-tabular-missing-descriptions.html . Seems outfmt descriptors are bit disorganized in the manual. But yes, its possible directly without parsing xml file. I'm now able to annotate eukaryotic proteins just with a simple BLASTp.